You should make your Flash file transparent. Typical code to import Flash file on page and make it transparent is (change with your path/file and edit width/height everywhere in code):
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','956','height','284','title','Banner','src','images/stories/Banner_3','wmode','transparent','quality','high','pluginspage','http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash','movie','images/stories/Banner_3' ); //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="956" height="284" title="Banner">
<param name="movie" value="images/stories/Banner_3.swf" />
<param name="quality" value="high" />
<param name="wmode" value="transparent" >
<embed src="images/stories/Banner_3.swf" quality="high" wmode="transparent" pluginspage="http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash" type="application/x-shockwave-flash" width="956" height="284"></embed>
</object>
</noscript>
