In IE 7 menu appears over the Flash:
In Firefox the menu appears under the Flash: (How can I fix this?!)
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Use z-index and set the menu to something like 100 and the flash movie to something in the negative like.....say -1.
Have you tried the iframe trick (i.e. floating an iframe behind the menu, thus putting hte flash layers behind.)
Enabling wmode=transparent is the way to go. But also note, that Firefox in Linux does not obey that, and the flash will always be on top.