Joshua,
Ken Task turned me on to this thread. He has helped tremendously in getting a handle on this automated backups issue.
But for me, it has been happening in ALL my previous moodle versions, to one extent or another. What I have NOT been able to do is to get out of a stalled backup and get things back to a state where the system will attempt another automated backup on a failed backup.
For example, I have 7 course I back up every day. Sometimes they all backup fine. But once they begin failing, where one of them reports "unfinished", then it seems to have a cascading effect on the rest of them. Eventually, all of them fail, and I am left wondering how I am supposed to get teh backups started again.
Ken suggests cleaning out the moodledata temp folder. My only recourse at this point is to run a manual automated backups with a cron job. This makes moodle happy and it then reports that the backups are then "OK" again.
So, what are YOU doing when your backups fail to reset the backup routine?