I've seen many people who write for similar problem, i.e. to remove a custom post type on the search box for "link to existing content" on the tinyMCE editor of Wordpress.
I've a reversed problem, I can see ONLY pages and posts.
I cannot see custom post types I've created, all with public set to true, publicly_queryable set to true, capability_type set to true, show_in_nav_menus set to true, and so on.
I've used the plugin "B09 Link to Existing Content", without results.
Why? What can I do? Maybe the problem is on declaration of the custom post type? I've created a php file included into functions.php of my theme. Is this the problem? Does I need to load custom post type in a different manner?