I recently had an issue displaying jQuery Media full-screen videos in Drupal 6. After a little research, reading some threads and some trial and error, I was able to successfully display videos in full-screen mode. The fix ended up being quite simple, but there didn't seem to be a lot of documentation so here it is.
This fix assumes that you you're using jQuery Media module and successfully playing the video through JW Player of similar.
1. Go to: Administer > Configuration > jQuery Media
2. Select Advanced Settings