by Ken Task.
Hmmmm ... maybe it is working ... from what I re-collect ...
Highly recommend setting autobackup to an alternative backup area ... NOT inside the new file system (ie, filedir of moodledata). If one needs to grant teachers access to backups, one can setup a file system repo and use a symlink to the 'alternate backup area' per teacher.
On first run, how would the auto backup mod of Moodle know if a course has been NOT be modified the past 3 days? On first run, noticed it does backup all of them (cept hidden). Then Moodle has the data for modification date and can calculate X days or other.
Run it again from the command line as you did before and see if there are some skipped.
Then wait a little bit and run it again.
'spirit of sharing', Ken