I did a factory reset, wiped my library on kobo totally out, synched, added the falseperiod to the config, sideloaded only a quarter of the books I had on it before and now the check in the synch box is finally gone.
I am really curious if that helped for good.
If the new firmware is released on the 26th, I'd still be able to send it back for a full refund, if all of this shouldn't work.