It sounds as if you're suffering from a corrupted database on the kobo. When you connect the Kobo to calibre what messages are produced? Is there one talking about a malformed database?
If that is the issue, you need to recreate that database, either by doing a reset of the device, or going to Settings | Accounts and selecting "Sign out" next to your Kobo account.
Unfortunately either option will result in you having to redo the setup.
It's curious that you are experiencing this issue; known problems causing this were resolved in current releases
What mods / patches are you using?
Are you ensuring that you cleanly eject the device from your PC and allow it to process new content?
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