by Tim Hunt.
Well done for finding that bug Joshua. That could well be the cause.
Have you managed to establish an exact time-line for what is happening? That might give some clues, but since you don't want to sit up all night, it would probably need to be re-constructed from log files. When cron runs, it outputs quite detailed log information, but it is not very standard where/if that it saved. Can you track it down?
The automated clean-up of 'old' backup data does have a config setting configtempdatafoldercleanup. Can you try making that longer, and see if that 'solves' the problem. Oh, I see. It seems to default to 7 days (the longest). That does not seem like a problem.
Very odd.