Flash always ontop of page content.
I had this problem today with Flash (SWF) content appearing ontop of a JTip popup. I tried changing the z-index within the CSS, but it didn't work, it took me a long time to discover what needed to be done to fix it, but basically it was quite easy;
1. Add the following parameter to the OBJECT tag:
<param name="wmode" value="transparent">
2. Add the following parameter to the EMBED tag: