Flash by default is shown on top of all other elements, independent of the z-index you have defined. To prevent this from happening add
wmode="opaque" to the embed script for your flash movie. With this setting applied flash will no longer be on top of all elements so your menu and other overlay elements will be displayed in front of the flash movie.
Eample:
<embed width="450" height="154" menu="true" loop="true" play="true" src="/Portals/0/CustomModule1.swf" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash"
wmode="opaque"></embed>
Please find additional information on this issue
here