where you defined the flash movie, set the ‘wmode’ to transparent. then where the container div for the dropdown list is defined in css assign a ‘z-index’ greater than 1.
flash is usually on top of the object stack in a web browser, so no dynamic layers can overlap, but giving the flash object’s wmode a value of transparency, and (but not necessarily) adjusting the z-index of the <div> or <ul> (whatever contains the menu) allows you to look ‘through’ the flash movie, where it appears behind a css navigation (example: http://www.mtxhome.com/products.aspx)
hope this helps