To my mind, this sounds like a corrupted database on the Kobo. Try a logout / login from the Settings | Account menu. This will have the unfortunate side-effects of removing all books from the database and making you go through the setup process again.
You can partially make it less painful by before hand, saving the .adobe-digital-editions to your PC and then, after the setup, copying the two files in it back to your Kobo. This will alleviate the need to redo the ADE authorization.