I'm assuming you have a SWF file embedded in an HTML file? If so you will need to give your SWF file a transparent value so the menu appears over it. So your code should look more like this. (See the bold for the transparent value)
Code:
<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="450"
height="80" align="top" >
<param name="wmode" value="transparent">
<param name="movie" value="yourFlashFile.swf" />
<param name="quality" value="low" />
<embed src="yourFlashFileswf" width="450" height="80" align="top" quality="high"
pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash"
wmode="transparent"></embed>
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