If you did a factory reset, any shelves that were synced to the Kobo server will be recreated during the set-up. As the shelf state of sideloaded books is not synced, then a lot of empty shelves will be recreated during the set-up. And there has been a bug that seems to be on the server side where deleted shelves are recreated. I don't know it that has been fixed or not. But, I did a factory reset last week on my Glo and they didn't appear.
The driver should be removing empty shelves as long as the options are set correctly. Could you run calibre in debug mode, connect the device and then post the debug log? I can look through it and hopefully see what is going on.
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