Yes, I've seen that issue in IE6, the top nav links don't show up in that particular skin as well as the 5contentpanes skin. I messed around with it for about an hour and couldn't figure out what was causing it either so if you come up with a fix please let me know. The only tip I would suggest is, try your experiments to fix it using the IESpecific.css. You can override any of the css from the main files there without affecting other browsers. You might try putting a border on the whole thing and see if that makes it show up.
I may take a look at it again myself sometime but have a lot of other things on my plate at the moment.