I was looking into the issue you are describing and think I have a way for you to isolate what is causing the issue. We have an article to do just that, named Mac OS X: How to troubleshoot a software issue found here: http://support.apple.com/kb/HT1199.
When you go to the article it has 2 links that have different steps depending on which item you click.
If it only happens in, say iTunes for example, then you want to click the first option. If it happens no matter where you watch any video, then you will want to click the second link.
All the best,