Issue regarding plugin instalation

What version of WordPress are you using? Did this just start happening on a site that was previously working or is it a brand new installation?

Try to access your server via SFTP or FTP, navigate to your wp-includes folder, and upload a copy of update.php from a fresh install of WordPress.

Can you confirm this ONLY happens on Beta?

What version are you using?

Hello Geoffrey Shilling and Ipstenu (Mika Epstein),

Thanks for the quick replay. I am using wordpress version 4.4.2 and it is the fresh install(not a update to old installation).

here is the code snipped of update.php

<?php
/**
 * A simple set of functions to check our version 1.0 update service.
 *
 * @package WordPress
 * @since 2.3.0
 */

/**
 * Check WordPress version against the newest version.
 *
 * The WordPress version, PHP version, and Locale is sent. Checks against the
 * WordPress server at api.www.ads-software.com server. Will only check if WordPress
 * isn't installing.
 *
 * @since 2.3.0
 * @global string $wp_version Used to check against the newest WordPress version.
 * @global wpdb   $wpdb
 * @global string $wp_local_package
 *
 * @param array $extra_stats Extra statistics to report to the www.ads-software.com API.
 * @param bool  $force_check Whether to bypass the transient cache and force a fresh update check. Defaults to false, true if $extra_stats is set.
 */
function wp_version_check( $extra_stats = array(), $force_check = false ) {
	if ( wp_installing() ) {
		return;
	}

	global $wp_version, $wpdb, $wp_local_package;
	// include an unmodified $wp_version
	include( ABSPATH . WPINC . '/version.php' );
	$php_version = phpversion();

	$current = get_site_transient( 'update_core' );
	$translations = wp_get_installed_translations( 'core' );

	// Invalidate the transient when $wp_version changes
	if ( is_object( $current ) && $wp_version != $current->version_checked )
		$current = false;

	if ( ! is_object($current) ) {
		$current = new stdClass;
		$current->updates = array();
		$current->version_checked = $wp_version;
	}

	if ( ! empty( $extra_stats ) )
		$force_check = true;

	// Wait 60 seconds between multiple version check requests
	$timeout = 60;
	$time_not_changed = isset( $current->last_checked ) && $timeout > ( time() - $current->last_checked );
	if ( ! $force_check && $time_not_changed ) {
		return;
	}

	/**
	 * Filter the locale requested for WordPress core translations.
	 *
	 * @since 2.8.0
	 *
	 * @param string $locale Current locale.
	 */
	$locale = apply_filters( 'core_version_check_locale', get_locale() );

	// Update last_checked for current to prevent multiple blocking requests if request hangs
	$current->last_checked = time();
	set_site_transient( 'update_core', $current );

	if ( method_exists( $wpdb, 'db_version' ) )
		$mysql_version = preg_replace('/[^0-9.].*/', '', $wpdb->db_version());
	else
		$mysql_version = 'N/A';

	if ( is_multisite() ) {
		$user_count = get_user_count();
		$num_blogs = get_blog_count();
		$wp_install = network_site_url();
		$multisite_enabled = 1;
	} else {
		$user_count = count_users();
		$user_count = $user_count['total_users'];
		$multisite_enabled = 0;
		$num_blogs = 1;
		$wp_install = home_url( '/' );
	}

	$query = array(
		'version'            => $wp_version,
		'php'                => $php_version,
		'locale'             => $locale,
		'mysql'              => $mysql_version,
		'local_package'      => isset( $wp_local_package ) ? $wp_local_package : '',
		'blogs'              => $num_blogs,
		'users'              => $user_count,
		'multisite_enabled'  => $multisite_enabled,
		'initial_db_version' => get_site_option( 'initial_db_version' ),
	);

	$post_body = array(
		'translations' => wp_json_encode( $translations ),
	);

	if ( is_array( $extra_stats ) )
		$post_body = array_merge( $post_body, $extra_stats );

	$url = $http_url = 'https://api.www.ads-software.com/core/version-check/1.7/?' . http_build_query( $query, null, '&' );
	if ( $ssl = wp_http_supports( array( 'ssl' ) ) )
		$url = set_url_scheme( $url, 'https' );

	$options = array(
		'timeout' => ( ( defined('DOING_CRON') && DOING_CRON ) ? 30 : 3 ),
		'user-agent' => 'WordPress/' . $wp_version . '; ' . home_url( '/' ),
		'headers' => array(
			'wp_install' => $wp_install,
			'wp_blog' => home_url( '/' )
		),
		'body' => $post_body,
	);

	$response = wp_remote_post( $url, $options );
	if ( $ssl && is_wp_error( $response ) ) {
		trigger_error( __( 'An unexpected error occurred. Something may be wrong with www.ads-software.com or this server’s configuration. If you continue to have problems, please try the <a href="https://www.ads-software.com/support/">support forums</a>.' ) . ' ' . __( '(WordPress could not establish a secure connection to www.ads-software.com. Please contact your server administrator.)' ), headers_sent() || WP_DEBUG ? E_USER_WARNING : E_USER_NOTICE );
		$response = wp_remote_post( $http_url, $options );
	}

	if ( is_wp_error( $response ) || 200 != wp_remote_retrieve_response_code( $response ) ) {
		return;
	}

	$body = trim( wp_remote_retrieve_body( $response ) );
	$body = json_decode( $body, true );

	if ( ! is_array( $body ) || ! isset( $body['offers'] ) ) {
		return;
	}

	$offers = $body['offers'];

	foreach ( $offers as &$offer ) {
		foreach ( $offer as $offer_key => $value ) {
			if ( 'packages' == $offer_key )
				$offer['packages'] = (object) array_intersect_key( array_map( 'esc_url', $offer['packages'] ),
					array_fill_keys( array( 'full', 'no_content', 'new_bundled', 'partial', 'rollback' ), '' ) );
			elseif ( 'download' == $offer_key )
				$offer['download'] = esc_url( $value );
			else
				$offer[ $offer_key ] = esc_html( $value );
		}
		$offer = (object) array_intersect_key( $offer, array_fill_keys( array( 'response', 'download', 'locale',
			'packages', 'current', 'version', 'php_version', 'mysql_version', 'new_bundled', 'partial_version', 'notify_email', 'support_email', 'new_files' ), '' ) );
	}

	$updates = new stdClass();
	$updates->updates = $offers;
	$updates->last_checked = time();
	$updates->version_checked = $wp_version;

	if ( isset( $body['translations'] ) )
		$updates->translations = $body['translations'];

	set_site_transient( 'update_core', $updates );

	if ( ! empty( $body['ttl'] ) ) {
		$ttl = (int) $body['ttl'];
		if ( $ttl && ( time() + $ttl < wp_next_scheduled( 'wp_version_check' ) ) ) {
			// Queue an event to re-run the update check in $ttl seconds.
			wp_schedule_single_event( time() + $ttl, 'wp_version_check' );
		}
	}

	// Trigger a background updates check if running non-interactively, and we weren't called from the update handler.
	if ( defined( 'DOING_CRON' ) && DOING_CRON && ! doing_action( 'wp_maybe_auto_update' ) ) {
		do_action( 'wp_maybe_auto_update' );
	}
}

/**
 * Check plugin versions against the latest versions hosted on www.ads-software.com.
 *
 * The WordPress version, PHP version, and Locale is sent along with a list of
 * all plugins installed. Checks against the WordPress server at
 * api.www.ads-software.com. Will only check if WordPress isn't installing.
 *
 * @since 2.3.0
 * @global string $wp_version Used to notify the WordPress version.
 *
 * @param array $extra_stats Extra statistics to report to the www.ads-software.com API.
 */
function wp_update_plugins( $extra_stats = array() ) {
	if ( wp_installing() ) {
		return;
	}

	global $wp_version;
	// include an unmodified $wp_version
	include( ABSPATH . WPINC . '/version.php' );

	// If running blog-side, bail unless we've not checked in the last 12 hours
	if ( !function_exists( 'get_plugins' ) )
		require_once( ABSPATH . 'wp-admin/includes/plugin.php' );

	$plugins = get_plugins();
	$translations = wp_get_installed_translations( 'plugins' );

	$active  = get_option( 'active_plugins', array() );
	$current = get_site_transient( 'update_plugins' );
	if ( ! is_object($current) )
		$current = new stdClass;

	$new_option = new stdClass;
	$new_option->last_checked = time();

	// Check for update on a different schedule, depending on the page.
	switch ( current_filter() ) {
		case 'upgrader_process_complete' :
			$timeout = 0;
			break;
		case 'load-update-core.php' :
			$timeout = MINUTE_IN_SECONDS;
			break;
		case 'load-plugins.php' :
		case 'load-update.php' :
			$timeout = HOUR_IN_SECONDS;
			break;
		default :
			if ( defined( 'DOING_CRON' ) && DOING_CRON ) {
				$timeout = 0;
			} else {
				$timeout = 12 * HOUR_IN_SECONDS;
			}
	}

	$time_not_changed = isset( $current->last_checked ) && $timeout > ( time() - $current->last_checked );

	if ( $time_not_changed && ! $extra_stats ) {
		$plugin_changed = false;
		foreach ( $plugins as $file => $p ) {
			$new_option->checked[ $file ] = $p['Version'];

			if ( !isset( $current->checked[ $file ] ) || strval($current->checked[ $file ]) !== strval($p['Version']) )
				$plugin_changed = true;
		}

		if ( isset ( $current->response ) && is_array( $current->response ) ) {
			foreach ( $current->response as $plugin_file => $update_details ) {
				if ( ! isset($plugins[ $plugin_file ]) ) {
					$plugin_changed = true;
					break;
				}
			}
		}

		// Bail if we've checked recently and if nothing has changed
		if ( ! $plugin_changed ) {
			return;
		}
	}

	// Update last_checked for current to prevent multiple blocking requests if request hangs
	$current->last_checked = time();
	set_site_transient( 'update_plugins', $current );

	$to_send = compact( 'plugins', 'active' );

	/**
	 * Filter the locales requested for plugin translations.
	 *
	 * @since 3.7.0
	 *
	 * @param array $locales Plugin locale. Default is current locale of the site.
	 */
	$locales = apply_filters( 'plugins_update_check_locales', array( get_locale() ) );

	if ( defined( 'DOING_CRON' ) && DOING_CRON ) {
		$timeout = 30;
	} else {
		// Three seconds, plus one extra second for every 10 plugins
		$timeout = 3 + (int) ( count( $plugins ) / 10 );
	}

	$options = array(
		'timeout' => $timeout,
		'body' => array(
			'plugins'      => wp_json_encode( $to_send ),
			'translations' => wp_json_encode( $translations ),
			'locale'       => wp_json_encode( $locales ),
			'all'          => wp_json_encode( true ),
		),
		'user-agent' => 'WordPress/' . $wp_version . '; ' . get_bloginfo( 'url' )
	);

	if ( $extra_stats ) {
		$options['body']['update_stats'] = wp_json_encode( $extra_stats );
	}

	$url = $http_url = 'https://api.www.ads-software.com/plugins/update-check/1.1/';
	if ( $ssl = wp_http_supports( array( 'ssl' ) ) )
		$url = set_url_scheme( $url, 'https' );

	$raw_response = wp_remote_post( $url, $options );
	if ( $ssl && is_wp_error( $raw_response ) ) {
		trigger_error( __( 'An unexpected error occurred. Something may be wrong with www.ads-software.com or this server’s configuration. If you continue to have problems, please try the <a href="https://www.ads-software.com/support/">support forums</a>.' ) . ' ' . __( '(WordPress could not establish a secure connection to www.ads-software.com. Please contact your server administrator.)' ), headers_sent() || WP_DEBUG ? E_USER_WARNING : E_USER_NOTICE );
		$raw_response = wp_remote_post( $http_url, $options );
	}

	if ( is_wp_error( $raw_response ) || 200 != wp_remote_retrieve_response_code( $raw_response ) ) {
		return;
	}

	$response = json_decode( wp_remote_retrieve_body( $raw_response ), true );
	foreach ( $response['plugins'] as &$plugin ) {
		$plugin = (object) $plugin;
	}
	unset( $plugin );
	foreach ( $response['no_update'] as &$plugin ) {
		$plugin = (object) $plugin;
	}
	unset( $plugin );

	if ( is_array( $response ) ) {
		$new_option->response = $response['plugins'];
		$new_option->translations = $response['translations'];
		// TODO: Perhaps better to store no_update in a separate transient with an expiry?
		$new_option->no_update = $response['no_update'];
	} else {
		$new_option->response = array();
		$new_option->translations = array();
		$new_option->no_update = array();
	}

	set_site_transient( 'update_plugins', $new_option );
}

/**
 * Check theme versions against the latest versions hosted on www.ads-software.com.
 *
 * A list of all themes installed in sent to WP. Checks against the
 * WordPress server at api.www.ads-software.com. Will only check if WordPress isn't
 * installing.
 *
 * @since 2.7.0
 * @uses $wp_version Used to notify the WordPress version.
 *
 * @param array $extra_stats Extra statistics to report to the www.ads-software.com API.
 */
function wp_update_themes( $extra_stats = array() ) {
	if ( wp_installing() ) {
		return;
	}
	global $wp_version;
	// include an unmodified $wp_version
	include( ABSPATH . WPINC . '/version.php' );

	$installed_themes = wp_get_themes();
	$translations = wp_get_installed_translations( 'themes' );

	$last_update = get_site_transient( 'update_themes' );
	if ( ! is_object($last_update) )
		$last_update = new stdClass;

	$themes = $checked = $request = array();

	// Put slug of current theme into request.
	$request['active'] = get_option( 'stylesheet' );

	foreach ( $installed_themes as $theme ) {
		$checked[ $theme->get_stylesheet() ] = $theme->get('Version');

		$themes[ $theme->get_stylesheet() ] = array(
			'Name'       => $theme->get('Name'),
			'Title'      => $theme->get('Name'),
			'Version'    => $theme->get('Version'),
			'Author'     => $theme->get('Author'),
			'Author URI' => $theme->get('AuthorURI'),
			'Template'   => $theme->get_template(),
			'Stylesheet' => $theme->get_stylesheet(),
		);
	}

	// Check for update on a different schedule, depending on the page.
	switch ( current_filter() ) {
		case 'upgrader_process_complete' :
			$timeout = 0;
			break;
		case 'load-update-core.php' :
			$timeout = MINUTE_IN_SECONDS;
			break;
		case 'load-themes.php' :
		case 'load-update.php' :
			$timeout = HOUR_IN_SECONDS;
			break;
		default :
			if ( defined( 'DOING_CRON' ) && DOING_CRON ) {
				$timeout = 0;
			} else {
				$timeout = 12 * HOUR_IN_SECONDS;
			}
	}

	$time_not_changed = isset( $last_update->last_checked ) && $timeout > ( time() - $last_update->last_checked );

	if ( $time_not_changed && ! $extra_stats ) {
		$theme_changed = false;
		foreach ( $checked as $slug => $v ) {
			if ( !isset( $last_update->checked[ $slug ] ) || strval($last_update->checked[ $slug ]) !== strval($v) )
				$theme_changed = true;
		}

		if ( isset ( $last_update->response ) && is_array( $last_update->response ) ) {
			foreach ( $last_update->response as $slug => $update_details ) {
				if ( ! isset($checked[ $slug ]) ) {
					$theme_changed = true;
					break;
				}
			}
		}

		// Bail if we've checked recently and if nothing has changed
		if ( ! $theme_changed ) {
			return;
		}
	}

	// Update last_checked for current to prevent multiple blocking requests if request hangs
	$last_update->last_checked = time();
	set_site_transient( 'update_themes', $last_update );

	$request['themes'] = $themes;

	/**
	 * Filter the locales requested for theme translations.
	 *
	 * @since 3.7.0
	 *
	 * @param array $locales Theme locale. Default is current locale of the site.
	 */
	$locales = apply_filters( 'themes_update_check_locales', array( get_locale() ) );

	if ( defined( 'DOING_CRON' ) && DOING_CRON ) {
		$timeout = 30;
	} else {
		// Three seconds, plus one extra second for every 10 themes
		$timeout = 3 + (int) ( count( $themes ) / 10 );
	}

	$options = array(
		'timeout' => $timeout,
		'body' => array(
			'themes'       => wp_json_encode( $request ),
			'translations' => wp_json_encode( $translations ),
			'locale'       => wp_json_encode( $locales ),
		),
		'user-agent'	=> 'WordPress/' . $wp_version . '; ' . get_bloginfo( 'url' )
	);

	if ( $extra_stats ) {
		$options['body']['update_stats'] = wp_json_encode( $extra_stats );
	}

	$url = $http_url = 'https://api.www.ads-software.com/themes/update-check/1.1/';
	if ( $ssl = wp_http_supports( array( 'ssl' ) ) )
		$url = set_url_scheme( $url, 'https' );

	$raw_response = wp_remote_post( $url, $options );
	if ( $ssl && is_wp_error( $raw_response ) ) {
		trigger_error( __( 'An unexpected error occurred. Something may be wrong with www.ads-software.com or this server’s configuration. If you continue to have problems, please try the <a href="https://www.ads-software.com/support/">support forums</a>.' ) . ' ' . __( '(WordPress could not establish a secure connection to www.ads-software.com. Please contact your server administrator.)' ), headers_sent() || WP_DEBUG ? E_USER_WARNING : E_USER_NOTICE );
		$raw_response = wp_remote_post( $http_url, $options );
	}

	if ( is_wp_error( $raw_response ) || 200 != wp_remote_retrieve_response_code( $raw_response ) ) {
		return;
	}

	$new_update = new stdClass;
	$new_update->last_checked = time();
	$new_update->checked = $checked;

	$response = json_decode( wp_remote_retrieve_body( $raw_response ), true );

	if ( is_array( $response ) ) {
		$new_update->response     = $response['themes'];
		$new_update->translations = $response['translations'];
	}

	set_site_transient( 'update_themes', $new_update );
}

/**
 * Performs WordPress automatic background updates.
 *
 * @since 3.7.0
 */
function wp_maybe_auto_update() {
	include_once( ABSPATH . '/wp-admin/includes/admin.php' );
	include_once( ABSPATH . '/wp-admin/includes/class-wp-upgrader.php' );

	$upgrader = new WP_Automatic_Updater;
	$upgrader->run();
}

/**
 * Retrieves a list of all language updates available.
 *
 * @since 3.7.0
 *
 * @return array
 */
function wp_get_translation_updates() {
	$updates = array();
	$transients = array( 'update_core' => 'core', 'update_plugins' => 'plugin', 'update_themes' => 'theme' );
	foreach ( $transients as $transient => $type ) {
		$transient = get_site_transient( $transient );
		if ( empty( $transient->translations ) )
			continue;

		foreach ( $transient->translations as $translation ) {
			$updates[] = (object) $translation;
		}
	}
	return $updates;
}

/**
 * Collect counts and UI strings for available updates
 *
 * @since 3.3.0
 *
 * @return array
 */
function wp_get_update_data() {
	$counts = array( 'plugins' => 0, 'themes' => 0, 'wordpress' => 0, 'translations' => 0 );

	if ( $plugins = current_user_can( 'update_plugins' ) ) {
		$update_plugins = get_site_transient( 'update_plugins' );
		if ( ! empty( $update_plugins->response ) )
			$counts['plugins'] = count( $update_plugins->response );
	}

	if ( $themes = current_user_can( 'update_themes' ) ) {
		$update_themes = get_site_transient( 'update_themes' );
		if ( ! empty( $update_themes->response ) )
			$counts['themes'] = count( $update_themes->response );
	}

	if ( ( $core = current_user_can( 'update_core' ) ) && function_exists( 'get_core_updates' ) ) {
		$update_wordpress = get_core_updates( array('dismissed' => false) );
		if ( ! empty( $update_wordpress ) && ! in_array( $update_wordpress[0]->response, array('development', 'latest') ) && current_user_can('update_core') )
			$counts['wordpress'] = 1;
	}

	if ( ( $core || $plugins || $themes ) && wp_get_translation_updates() )
		$counts['translations'] = 1;

	$counts['total'] = $counts['plugins'] + $counts['themes'] + $counts['wordpress'] + $counts['translations'];
	$titles = array();
	if ( $counts['wordpress'] )
		$titles['wordpress'] = sprintf( __( '%d WordPress Update'), $counts['wordpress'] );
	if ( $counts['plugins'] )
		$titles['plugins'] = sprintf( _n( '%d Plugin Update', '%d Plugin Updates', $counts['plugins'] ), $counts['plugins'] );
	if ( $counts['themes'] )
		$titles['themes'] = sprintf( _n( '%d Theme Update', '%d Theme Updates', $counts['themes'] ), $counts['themes'] );
	if ( $counts['translations'] )
		$titles['translations'] = __( 'Translation Updates' );

	$update_title = $titles ? esc_attr( implode( ', ', $titles ) ) : '';

	$update_data = array( 'counts' => $counts, 'title' => $update_title );
	/**
	 * Filter the returned array of update data for plugins, themes, and WordPress core.
	 *
	 * @since 3.5.0
	 *
	 * @param array $update_data {
	 *     Fetched update data.
	 *
	 *     @type array   $counts       An array of counts for available plugin, theme, and WordPress updates.
	 *     @type string  $update_title Titles of available updates.
	 * }
	 * @param array $titles An array of update counts and UI strings for available updates.
	 */
	return apply_filters( 'wp_get_update_data', $update_data, $titles );
}

/**
 * @global string $wp_version
 */
function _maybe_update_core() {
	global $wp_version;
	include( ABSPATH . WPINC . '/version.php' ); // include an unmodified $wp_version

	$current = get_site_transient( 'update_core' );

	if ( isset( $current->last_checked, $current->version_checked ) &&
		12 * HOUR_IN_SECONDS > ( time() - $current->last_checked ) &&
		$current->version_checked == $wp_version ) {
		return;
	}
	wp_version_check();
}
/**
 * Check the last time plugins were run before checking plugin versions.
 *
 * This might have been backported to WordPress 2.6.1 for performance reasons.
 * This is used for the wp-admin to check only so often instead of every page
 * load.
 *
 * @since 2.7.0
 * @access private
 */
function _maybe_update_plugins() {
	$current = get_site_transient( 'update_plugins' );
	if ( isset( $current->last_checked ) && 12 * HOUR_IN_SECONDS > ( time() - $current->last_checked ) )
		return;
	wp_update_plugins();
}

/**
 * Check themes versions only after a duration of time.
 *
 * This is for performance reasons to make sure that on the theme version
 * checker is not run on every page load.
 *
 * @since 2.7.0
 * @access private
 */
function _maybe_update_themes() {
	$current = get_site_transient( 'update_themes' );
	if ( isset( $current->last_checked ) && 12 * HOUR_IN_SECONDS > ( time() - $current->last_checked ) )
		return;
	wp_update_themes();
}

/**
 * Schedule core, theme, and plugin update checks.
 *
 * @since 3.1.0
 */
function wp_schedule_update_checks() {
	if ( ! wp_next_scheduled( 'wp_version_check' ) && ! wp_installing() )
		wp_schedule_event(time(), 'twicedaily', 'wp_version_check');

	if ( ! wp_next_scheduled( 'wp_update_plugins' ) && ! wp_installing() )
		wp_schedule_event(time(), 'twicedaily', 'wp_update_plugins');

	if ( ! wp_next_scheduled( 'wp_update_themes' ) && ! wp_installing() )
		wp_schedule_event(time(), 'twicedaily', 'wp_update_themes');

	if ( ( wp_next_scheduled( 'wp_maybe_auto_update' ) > ( time() + HOUR_IN_SECONDS ) ) && ! wp_installing() )
		wp_clear_scheduled_hook( 'wp_maybe_auto_update' );
}

/**
 * Clear existing update caches for plugins, themes, and core.
 *
 * @since 4.1.0
 */
function wp_clean_update_cache() {
	if ( function_exists( 'wp_clean_plugins_cache' ) ) {
		wp_clean_plugins_cache();
	} else {
		delete_site_transient( 'update_plugins' );
	}
	wp_clean_themes_cache();
	delete_site_transient( 'update_core' );
}

if ( ( ! is_main_site() && ! is_network_admin() ) || ( defined( 'DOING_AJAX' ) && DOING_AJAX ) ) {
	return;
}

add_action( 'admin_init', '_maybe_update_core' );
add_action( 'wp_version_check', 'wp_version_check' );
add_action( 'upgrader_process_complete', 'wp_version_check', 10, 0 );

add_action( 'load-plugins.php', 'wp_update_plugins' );
add_action( 'load-update.php', 'wp_update_plugins' );
add_action( 'load-update-core.php', 'wp_update_plugins' );
add_action( 'admin_init', '_maybe_update_plugins' );
add_action( 'wp_update_plugins', 'wp_update_plugins' );
add_action( 'upgrader_process_complete', 'wp_update_plugins', 10, 0 );

add_action( 'load-themes.php', 'wp_update_themes' );
add_action( 'load-update.php', 'wp_update_themes' );
add_action( 'load-update-core.php', 'wp_update_themes' );
add_action( 'admin_init', '_maybe_update_themes' );
add_action( 'wp_update_themes', 'wp_update_themes' );
add_action( 'upgrader_process_complete', 'wp_update_themes', 10, 0 );

add_action( 'update_option_WPLANG', 'wp_clean_update_cache' , 10, 0 );

add_action( 'wp_maybe_auto_update', 'wp_maybe_auto_update' );

add_action( 'init', 'wp_schedule_update_checks' );

I’ve moved this out of alpha/beta. If you’re not testing the new versions of WordPress core, your post doesn’t belong there.

Beside the maximum execution time, there are other timeouts imposed in WordPress code. If you are comfortable with changing WordPress PHP files, then you can eliminate this problem by changing the timeout value in line 279 of wp-includes\update.php from 3 to 10 or so.
was: $timeout = 3 + (int) ( count( $plugins ) / 10 );
should be: $timeout = 10 + (int) ( count( $plugins ) / 10 );

You can anticipate encountering other similar errors due to timeouts. This is a list of low timeout values that I found in the code so far:
wp-includes/update.php (112)
wp-admin/includes/update.php (110)
wp-admin/includes/translation-install.php (44)

Just another thought. The timeout values in the WordPress PHP code should be OK if the network connection works well, and particularly the DNS name resolution. It would be more advisable to find the network bottleneck that is causing the delays rather then hacking the PHP code.
In my case, I found that the Virtualbox DNS resolution was slow (I was running an Ubuntu development server for WordPress in Virtualbox). After changing the guest OS’s /etc/resolv.conf to external DNS servers, the lags disappeared and the timeouts no longer occurred.