I'm currently working on a live video-chat solution named Butterflive (more on that later).
The chat window is a div with absolute positionning. When the chat window was moved above a flash video (a SWF), I noticed strange results (see below).

You can see that some parts of the chat window are going above and some parts are going below the Flash movie.
I tried to tweak the zindex CSS property without any success.
Actually, the problem comes from Flash.