My advice is obviously too late for you but may help others. I had the same issue and basically just waited it out because I knew that at the end of 10 days (length of all of our auctions) things would work themselves out.

If anyone doesn't want to wait that long you probably just need to go in and edit the names of the categories on the eBay side to match the order of those in AW2K. Remember ... eBay and AW2K are just communicating the numbers, not the names.