I had been noticing problems with embedded youtube videos lately with IE9 also. I would click an embedded video and the progress bar would move, and I would hear the sound of the video (if it had any) but no video. I learned that clicking on the 'full screen' button would make the video appear. I of course then had to hit 'esc' to go back to normal size, but this has been my workaround for a few days now.
I'll try the 'trusted sites' thing when I get home. I'm @ work now, on XP w/ IE7 :-(