yeah thats a known problem. Thats why the ad used to be above the nav in the old site. However the advertisers wanted it there, so theres not much we can do about it. Its only an intermittent bug (some ads are designed so they have a higher Z order to stop people hiding them)
But I have one observation, on my Windows machine I do not have any such problem, both in IE 8 beta as well as Firefox.
I encountered this problem only in my Firefox + OpenSuse combination (with Adblock Plus disabled of course). But then I also have the same problem with facebook too while playing the flash games, the menu tends to go behind the flash.