Via Erol and on Xander's Blog:
The solution to display a div on top off flash for the newer browser is the wmode option opaque or transparent.
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,29,0" width="100" height="200">
<param name="movie" value="test.swf" />
<param name="quality" value="high" />
<param name="wmode" value="opaque" />
<embed src="matrix.swf" width="100" height="200" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" wmode="opaque"></embed>
</object>
The following browsers currently support windowless mode:
Windows and Mac OS X
Internet Explorer 3 or higher (Windows)
Internet Explorer 5.1* and 5.2* (Macintosh)
Netscape 7.0*
Mozilla 1.0 or higher*
AOL*
CompuServe*
* Macromedia Flash Player version 6,0,65,0 (Windows) or 6,0,67,0 (Macintosh) or higher required for this feature.
Read what Macromedia writes about this subject: Flash content displays on top of all DHTML layers -> http://www.macromedia.com/go/tn_15523