Those symptoms of a corrupt database on the device. The status of books is stored in the database, and if it is corrupted, reading the database does not give the expected results. And any updates do not get stored properly. Hence the reading position is forgotten and any books added do not get put into the database during the processing. If you use calibre, it will probably give an error when trying to access the device.
Unfortunately, the fix is to sign out of your Kobo account on the device. This will replace the current database with an empty one and take you through the setup steps. After logging in, the sideloaded books will be reprocessed. You will also need to reauthorise the device using ADE.
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