Well, no one seems to be venturing guess here, so I'll begin ...
From what I've learned about autobackups ... Moodle uses first moodledata/temp/backup/ as a build area to make the backups. Check that area for residual files/folders remaining - should only be 0 byte .log files with loooooong file names - which indicate success. If you see any greater then 0 .log files open and inspect. Might be a clue in there. It is safe to manually remove all files folders inside the backup directory.
Once the backup file has been built, Moodle then copies (not move) the built .mbz file to the designated folder. You've said this is on another server so am guessing thats a mount point. It's been my experience that courses of 4.x+ Gig size have issues with being copied (not moved) on a CentOS system (if running RHEL) probably the same. Has to do with kernel and there is a fix, but one would have to re-compile kernel to get that support.
In the DB (version 2.5), there are three tables related to backups:
mdl_backup_controllers, mdl_backup_courses, and mdl_backup_files_template. Check the first two tables for info ... the last usually contains nothing.
Check out the first table for info. It would be rare probably but maybe, just maybe, some instructors are running backups of their own courses (snow balls chance, but ...).
Think autobackups would be run by user 2 - that's the admin account.
Courses that have not changed within the config limits are not backed up but skipped ... one can see that while running cron. Also, there is a command line utility just for autobackups in /moodlecode/admin/cli/ which might be worth running to see what's going on.
'spirit of sharing', Ken