I'm sure its due to some other difference I didn't appreciate yet... don't think you should have to re-install...
Did we already discuss which version of zen cart you are using?
But lets check to make sure its the stylesheet.
Save a copy of your stylesheet somewhere, and in its place, upload my apple zen stylesheet, and see if the problem persists. Then we'll know for sure its something in the stylesheet.
I'm attaching a text file with my stylesheet. It would probably look REALLY crazy, but if you go to a product page you should be able to see if the menu is over or under. Here is the file:
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