I'm not sure what the cause could be. I've also had a problem where I'm working on a stale copy of the dialogue and when I save it, nothing changes in the game. I have to go to the dialogue manager and click the edit button again to see the current version. Maybe these problems are related?
That error means the Dialogue Editor's auto-backup feature wasn't able to delete the old auto-backup copy of the database to create a new one. Is something holding onto the backup file? Can you delete it by hand? (Make sure you don't need it first.)
You can turn off auto-backups by going to the Database tab and changing Editor Settings > Auto Backup Frequency to 0. You won't get the error any more, but that's because the editor won't be making auto-backups.
The other issue you described could be related. If you can delete the old backup file by hand, maybe that will clear it up.