I have seen this type of behavior in sites that use Flash before. The fix is usually two part, the first part is to adjust any css and z-index that may affect this. It sounds like you have adjusted the z-index but you should check the positioning of the divs. If they do not have the same positioning the z-index will not work out properly.
The other thing that is the major cause of this is not have the wmode property set properly. Setting the wmode parameter to have a value of transparent should make it behave correctly. This has been the problem in most of the cases where I have seen this issue. There is a lot of info about this setting around on the web.
