Ok, I got tired of waiting for a fix, so I investigated it myself. I suspected it was the z-order but was thrown off because DoMiN8ToR said it would take a site redesign to fix this. So I thought it couldn't be something so simple...
I saved the source for the main page and I tried to figure out what the ad actually was.
When I removed the <div id="cache_ad"> part, the ad disappeared. So I tried to add a style="z-index:0" to the div, but still the menu's were popping under the ad.
I dumped menujs.php to a file and fixed the saved index file so it would load the local file instead from the cdfreaks website.
document.write('<DIV ID="m1" class="m1">');
document.write('<DIV ID="m1" class="m1" style="z-index: 1">');
And now the first menu works.. No 2 month site redesign needed, just 10 minutes work. Now PLEASE fix this rather annoying bug.. thank you.
I have no idea if MSIE users are plagued by this too, but the fix should work for MSIE too in that case.