I’m having the same issue and cant’ figure it out. I’m assuming because I just upgraded to WP 3.3.1 I use primarily vimeo videos but have test it with youtube. The videos go full-screen on vimeo using https://player.vimeo.com/video/20902838. I’ve also tried just using the non-embed code and it link takes you directly to vimeo. https://vimeo.com/20902838
Nextgen and Shadwobox js are activated. Strangely the the code
<?php wp_head(); ?>
shows up in the editor but when looking at the source code through a browser, it doesn’t show up. Not sure if it’s supposed to or not.