Which format of books are using? Ones that you synchronize via the Kobo Desktop, or ones via Adobe Digital Editions?
If Kobo Desktop, it is possible that you have a corrupted Sqllite database on the Kobo; you will find instructions in http://www.mobileread.com/forums/showthread.php?t=94789
on how to replace the database.
You might also want to double check the time / date settings on the Kobo. Not sure if that would affect syncing, but it can't help to double check.
It sounds like you might have a corrupted database on the Kobo.