I run a bunch of store items and had a similar experience until I figured out that AW2K doesn't match the store categories by name, but by numeric order.

Just go into your "manage my Ebay store", and then "edit store". Make a note of the exact order of your 11 categories. Then edit your store categories in AW2K and make sure they are in the exact same order (as I discovered, it doesn't even matter what you call the categories in AW2K - all that matters is the order).

Once I figured this out, I never had to edit a store item's category again.

The same thing applies to regular auction items - you can have them show up in your matching store categories as well. (If you don't specify a category for regular auctions, they all end up in the "other" category).

Hope that helps!
Rich