When the menus appear behind a Flash element on the page it is likely do to the wmode setting of the Flash on the page. Here is a kb article from Adobe that discuses this and how to resolve it.
viewContent.do?externalId=tn_15523
Along with the wmode you can control the stacking order further by using the z-index along with the positioning. If two elements on a page are set to the same positioning, like relative, then the z-index will determine their stacking order.