I spent a lot of time scouring the web for a solution to this 'javascript menu appearing behind flash' problem. The advice that Katarey and many on the web suggest did not work for me:
1. Add the following parameter to the OBJECT tag:
<param name="wmode" value="transparent">
2. Add the following parameter to the EMBED tag:
wmode="transparent"
Until I found this post: http://www.likno.com/blog/my-submenu-is-not-appearing-over-a-flash-element-what-can-i-do/227/
The solution was to add ONE MORE (3 total) 'wmode' line to your AC_FL_RunContent script. This assumes that you're using the Adobe/Macromedia method of embedding your flash objects.
My code:
<script type="text/javascript">
AC_FL_RunContent( 'codebase','http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,28,0','width','700','height','600','title','title of my flashmovie','src','/swf/flashfilename','quality','high','pluginspage','http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash','movie','/swf/flashfilename','wmode','Transparent' ); //end AC code
</script>
<noscript>
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,28,0" width="700" height="600" title="title of my flashmovie">
<param name="movie" value="/swf/flashfilename.swf">
<param name="quality" value="high">
<param name="wmode" value="transparent">
<embed src="/swf/flashfilename.swf" wmode="transparent" quality="high" pluginspage="http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash" type="application/x-shockwave-flash" width="700" height="600"></embed>
</object>
</noscript>
And between the and tags, don't forget to add:
<script src=”AC_RunActiveContent.js” language=”javascript”></script>
Flash will generate this file for you.. or you could download it from the Macromedia site.