The WYSIWYG editor can loose functionality if you deregister the WordPress default jQuery via:
wp_deregister_script( 'jquery' );
In fact a lot of screwy things can happen to the admin when you do this. However, lot’s of us want to use our own version of jQuery for our themes / plugins. The solution is to deregister the default jQuery only if the admin is not active. To do this, put the following in your theme’s functions.php file:
if(!is_admin()) {
wp_deregister_script( 'jquery' );
wp_register_script('jquery', '/your/server/path/to/jquery.js');
}
Now, you can put
wp_enqueue_script('jquery');
in your header.php file and it will call your preferred jQuery version for your theme, but the admin will utilize the default jQuery as it’s designers intended.