I thought you meant they're not showing up in searches. Ok, are they store items and they aren't going into the categories in your eBay store? Do I have that right? If so, when you're creating the store listing, are you selecting main and secondary store categories? That may sound like a dumb question but I missed this when I first started, which is why I'm asking. I don't know what else would cause them to not categorize correctly other than these things though.
To clarify about the search... the way I check is to view my own other listings to see when they become searchable. Once they show there, I know others can see them too. The store categories should have nothing to do with it if you can already see them in the store and beyond My eBay.