The problem is that Flash is the dominatin feature on any web site. Nothing else will ever open on top of it, just underneath it. So simply make sure that when your nav bar pop ups are in full view, they are not trying to pop up on top of the flash. This will never happen. You just need to make sure you have your spacing right.
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Capone De Leon
Head of Design
http://www.ManJonStudios.com
Student of the net in constant search of "The WOW".
A Zen like state in which creativity, talent, hard work and dedication
create an amazing web site with a life all its own!
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