Shadowbox, Thickbox – affecting Featured Post Slideshow

The theme I’m using on a website has the use of a Featured Post slideshow, which I had set up and working perfectly.

I now need to add a youtube gallery with the ability of opening in page with something like Shadowbox, Thickbox etc.

When I activate one of these plugins the Featured Image slide show on the homepage breaks and the images just sit one on top of the other.

I have read a few things on here regarding JQuery but I can’t see any in the code for the Featured Slideshow.

Can anyone tell me why this is happening ?

Home Page Featured Image Code

<?php
if(get_theme_option('featured_posts') != '') {
?>
<script type="text/javascript">
	function startGallery() {
		var myGallery = new gallery($('myGallery'), {
			timed: true,
			delay: 6000,
			slideInfoZoneOpacity: 0.8,
			showCarousel: false
		});
	}
	window.addEvent('domready', startGallery);
</script>
<div class="fullbox_excerpt">
	<div class="fullbox_content">
		<div class="smooth_gallery">
			<div id="myGallery">

				<?php
				$featured_posts_category = get_theme_option('featured_posts_category');

				if($featured_posts_category != '' && $featured_posts_category != '0') {
					global $post;

					 $featured_posts = get_posts("numberposts=5&&category=$featured_posts_category");
					 $i = 0;
					 foreach($featured_posts as $post) {
					 	setup_postdata($post);
                        if ( version_compare( $wp_version, '2.9', '>=' ) ) {
                            $slide_image_full = get_the_post_thumbnail($post->ID,'large', array('class' => 'full'));
                            $slide_image_thumbnail = get_the_post_thumbnail($post->ID,'large', array('class' => 'thumbnail'));
                        } else {
                            $get_slide_image = get_post_meta($post->ID, 'featured', true);
                            $slide_image_full = "<img src=\"$get_slide_image\" class=\"full\" alt=\"\" />";
                            $slide_image_thumbnail = "<img src=\"$get_slide_image\" class=\"thumbnail\" alt=\"\" />";
                        }

					  ?>
					  <div class="imageElement">
							<h3><?php the_title(); ?></h3>
							<?php the_excerpt(); ?>
							<a href="<?php the_permalink(); ?>" title="<?php the_title(); ?>" class="open"></a>
							<?php echo  $slide_image_full; ?>
							<?php echo  $slide_image_thumbnail; ?>
						</div>
					 <?php }
				} else {
					for($i = 1; $i <=5; $i++) {
						?>
							<div class="imageElement">
								<h3>This is featured post <?php echo $i; ?> title</h3>
								<p>To set your featured posts, please go to your theme options page in wp-admin. You can also disable featured posts slideshow if you don't wish to display them.</p>
								<a href="#" title="This is featured post <?php echo $i; ?>" class="open"></a>
								<img src="<?php bloginfo('template_directory'); ?>/jdgallery/slides/<?php echo $i; ?>.jpg" class="full" alt="" />
								<img src="<?php bloginfo('template_directory'); ?>/jdgallery/slides/<?php echo $i; ?>.jpg" class="thumbnail" alt="" />
							</div>
						<?php
					}
				}

				?>
			</div>
		</div>
	</div>
</div>
<?php } ?>

Shadowbox code

<?php
/*
Plugin Name: Shadowbox
Plugin URI: https://ilbonzo.org
Description: Questo plugin integra in wordpress le funzionalità di shadowbox di Michael J. I. Jackson.
Author: Matteo Magni
Version: 0.2
Author URI: https://ilbonzo.org
 */

/* Copyright 2008 Matteo Magni (email: [email protected])
  This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
   GNU General Public License for more details.
      You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 */

function shadowbox_init() {
	$url = get_bloginfo('wpurl');
?>
<!-- WP shadowbox Plugin version 0.2 -->
<link rel="stylesheet" href="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/css/shadowbox.css" type="text/css" media="screen" />

<?php
/* ############################################### MOOTOOLS ########################################### */
?>

<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/lib/mootools.js"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/adapter/shadowbox-mootools.js"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/shadowbox.js"></script>

<script type="text/javascript">

window.onload = function(){

    Shadowbox.init();

    var flash_els = [
        document.getElementById('flash1'),
        document.getElementById('flash2'),
        document.getElementById('flash3')
    ];

    Shadowbox.setup(flash_els, {
        gallery:        'Flash',
        continuous:     true,
        counterType:    'skip'
    });

};

</script>

<?php
/* ################################# PROTOTYPE #################################### */
/*
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/lib/prototype.js"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/lib/scriptaculous/scriptaculous.js?load=effects"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/adapter/shadowbox-prototype.js"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/shadowbox.js"></script>

<script type="text/javascript">

document.observe('dom:loaded', function(){Shadowbox.init();});

</script>

*/?>

<?php
/* ################################# YUI #################################### */
/*
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/lib/yui-utilities.js"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/adapter/shadowbox-yui.js"></script>
<script type="text/javascript" src="<?php echo $url; ?>/wp-content/plugins/shadowbox/src/js/shadowbox.js"></script>

<script type="text/javascript">

YAHOO.util.Event.onDOMReady(Shadowbox.init);

</script>

<script type="text/javascript">

window.onload = Shadowbox.init;

</script>

*/
?>

<?php

}

//add Action
add_action('wp_head', 'shadowbox_init');
?>