Guess either I didn't explain nor it was missed ... but what I did was to clear in tables related to backups ... leaving the tables, just removed all data in them.
Believe the proper DB admin terminology is 'truncated'.
I then also made sure there was nothing left in moodledata/temp/backup/ that was from a former attempt at backing up anything ... that directory contained nothing.
I then check the defaults for course backups - settings like include users, etc. Choose NOT to include logs of the courses there.
Then ran one command line backup of one course and pointed it to a diretory OUTSIDE of the Moodle file system to assure that tables had data, backup ran and used moodledata/temp/backup (watched it real time from terminal using 'watch' command).
Untared the .mbz backup in that designated directory and inspected the xml's and compared with the directory contents ... everything there checked out ... so now the next step
Setting auto-backups to manual ... still pointed to designated diretctory outside of Moodle file system so I could, if desired, un-tgz them and inspect.
Now to see those backups in the Moodle interface, used a file system repo (moodledata/repository/) and created a symlink for backups which pointed the designated directory outside of moodledata. That is a linux thing but assume one could do same on Winders.
One thing ... I have the automated backups in Moodle onfig set to manual and in a bash shell script. At first I ran it 'manually' ... from command line - at least once to see it all working ... checking tables, etc. Then and only then did I do a cron job (outside of Moodle but an opertating system cron job) to run the autobackups script.
Now in many of the systems I help admin, there are 3-5 courses that are soooooo large, anything automated chokes ... not enough time to run it ... etc.. (despite making all sorts of changes to PHP, etc..) ... so I actually have two of those bash shell scripts the run through a loop file consisting of only the course ID numbers to run the backup.php script found in moodlecode/admin/cli/
Whew! That's a mouth full and am getting the same 'brain cramps' I got when thinking this through and setting it up! Asprin is in order now! :\
Hope that clarifies some things.
What Joshua has discovered, I think, is a conflict between when he's scheduled the autobackups with other jobs one can now schedule in Moodle 2.9 ... that of the clean up of the backup directory.
If the auto backup is running and this other task/cron job executes and cleans out files/directories in moodledata/temp/backup/ then the auto backup can't complete ... or if it does, it's missing files ... like moodle_backup.xml (very important file as it's the road map to the whole thing!).
So while we're talking backups there are some circumstances/setups that will work against the other. I frankly don't know how a large system can do autobackups and schedule the clean up task/cron job to NEVER interfere with the completion ...
Bottom line ... I have somthing workable but it's not via the Moodle Admin UI ... where it should be for most folks. ;)
'spirit of sharing'. Ken