Hello!
Sorry for the silence, I was experimenting with rebuilds that take their time. The reason for the strange DB behaviour is that the backup broke with the previous Beta, and I usually managed to repair backups by deleting problem files and then rebuilding the database. This didn’t work in this case, and that caused the imbalance in the backend.
I managed to get it all going again, deleting backup versions made the file differences decrease, and after having deleted around half of the versions it seems to be working all right.
Hopefully the new release will be more stable. Thanks for your tips and help! 
Rickard