I had an issue with thickbox where it would show the image behind a flash video in FireFox. IE7 worked great. I ran across Sheriar Designs Blog posting a fix specifically for DHTML menus over a flash video. I figured I would give it a try and much to my surprise, the suggestion worked! I give ALL CREDIT to the author of the blog, Mani (Pronounced like Bonnie, not Mani like Danny)
I merely wanted to blog the information for my own record keeping, plus to help 'index' the solution for others.
Update 2011/12/18: I ran into the same issue using Youtube's new iframe format and Colorbox... After running across a post on maxmorgandesign.com, the solution is pretty simple: Simply add ?wmode=transparent
<iframe width="420" height="315" src="http://www.youtube.com/embed/nGeKSiCQkPw?wmode=transparent" frameborder="0" allowfullscreen></iframe>
I'm assuming this also works with Thickbox and it doesn't appear to require any special css magic!