In case anyone else has this same issue, I wanted to post an alternative solution that was better for our situation. Simply set the wmode parameter for Flash to transparent. Examples:
TRADITIONAL EMBED:
<param name="wmode" value="transparent" />
AC_FL_RUNCONTENT:
AC_FL_RunContent( 'codebase','http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,28,0','width','900','height','1000','title','test','src','animation','quality','high','pluginspage','http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash','movie','animation','wmode','transparent' );
SWFObject:
swfobject.embedSWF("animation.swf", "animation", "300", "120", "9.0.0","expressInstall.swf", '', {wmode:"transparent"}, {id:"animation",name:"animation"});