By CSS set the z-index="2" to the java menu and a layer that contains the flash set z-index="1", this should make the zindex with higher number being displayed in top of the lower ones.

More important:

add this parameter to the flash object (each flash param is present in 2 locations):

WMODE = TRANSPARENT

It worked on other sites even though WMODE is normally for something else.

Code should look like this, Note that Wmode is in 2 locations:

<div style="z-index:2;">
JAVA SCRIPT MENU HERE
</div>

<div style="z-index:1;">
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0" width="200" height="100">
<param name="movie" value="flash_button.swf" />
<param name="quality" value="high" />
<param name="wmode" value="transparent" />
<embed src="flash_button.swf" width="200" height="100" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" wmode="transparent"></embed>
</object>
</div>

[edited by: adrianTNT at 12:46 pm (utc) on Nov. 11, 2006]