Sometimes if you use flash and javascript on the same page, you will have some problem with your layers or javascript. The most common problem is that the javascript menu or other control goes behind the flash file. I am sure you have tried many things like changing the z-index or putting flash more down but the solution is simpler than that. How? You have to make your flash transparent and everyting will be okay.

A Css Menu is displayed using Css classes while all the links in the Javascript menu are embedded in the JavaScript file. Following is an example of displaying a Css Markup Menu