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From the second post, I think the database on the device is corrupt. This stores information about the books including the reading status. That status is used to work out which book the cover should be displayed for.
The fix for this is to logout on the device. This replaces the current database with a new one and then repopulates it from the books on the device. You will lose the reading status, but that isn't being maintained properly anyway. You can try my Kobo Utilities plugin in calibre to store and restore the reading status, but I suspect it won't be able to read the database any more.
If that isn't it, then some more information is needed. What firmware? Are the books on the SD card? What book format? As you mention calibre, are you using the extended driver?
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