I remember a thread last week that had a similiar issue:
In that case, however, it was a little more clear that there was some kind of database corruption behind the issue. You don't seem to be experience the more exotic symptoms that user had, so I'm not sure.
Have you tried a sync using the official desktop tool? that seems to reset/rebuilt a part of the database, worth a shot anyway.
In the worst case, you might be forced to just delete the database and start fresh. You will lose the 100 pre-loaded books, but that's not really a huge deal, you can get them all back from Project Gutenburg
. There are instructions how to do this on the Kobo FAQ some of us have started to polish up recently: How do I get rid of the 100 free books installed on my new Kobo?
As a side note, I have heard a few people mention that tech support has provided people with a download link to re-downloaded the 'base' Kobo files after they have accidentally deleted them. It might just be hearsay... maybe Sameer can comment on this?
@Sammer: Can you provide any insights into if/when you guys are going to provide us with some maintenance tools to rebuilt/clean-up/sanity-check the SQLite dbase?