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OK, there's the question I forgot to ask... Is your Borders App updated, as well? My Kobo Desktop app is version 1.8, and I used it to update my Kobo. If you have an old app, I suspect that would foul up your database. Also, I did not replace my database with the 1.8 database (supplied in a sticky here), and I am having the now documented problems with repeated text. I haven't connected to Calibre (I just drag 'n drop my books to sideload), so I don't know if I would get the same errors you have. I will have to replace my database before I do much more reading with my Kobo.
So there are couple of possibilities to check - your Borders version, and replace the database and reload all your books - synced and sideloaded.
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