Hi,
Your site is looking good.
The first thing I would do is try to whip your code into XHTML validation - At least, thats where I usually start any debugging. When trying to validate it, I was returned with:
Failed validation, 23 errors.
Anyhow, you might try adding this:
embed#rotator, p#player {z-index:1;}
to your CSS file to solve the problem.
It is difficult to say what the actual culprit may be.
Typically, CSS menus that do this can be easily fixed by adding "wmode:transparent" to the Flash (which is already hardcoded into FR) or the z-index can be made lower.
The template you are using is loaded with several javascripts, and the menus seems to be a jvascript/CSS hybrid so there's really no telling where it conflicts.
As you can see
here, the true CSS menus work fine, so you may want to look into a bypass if you must use the rotator..or any other Flash for that matter.
Best of luck