The easiest fix is with the Z-Index in the CSS. For some reason, different browsers interpret levels slightly different with objects and flash - regardless of whether you have transparent marked.
So what you need to do is first take the div that wraps your menu (I am assuming it is within a div)... for example:
(php include for menu here)
Then in your CSS, you would need two changes:
Please note, you have to invoke the position attribute for z-index to work... Z-Index is completely arbitrary, you can set the number to whatever you want... the highest number always shows on top.
If you still have an issue, you need to take the div that holds your flash and do the same thing and explicitly set the number in your z-index lower than the number in your menu like this: