by Ken Task.
I see quickmail_block early on in the bug report. Suggest checking into permissions/etc. concerning that block in the troubled courses.
Also, as a test, taking just one course that has the issue and removing the quickmail block ... safe to do, I think, cause you can always add it back again.
If you have command line access one could run the automated backups via command line: /moodlecode/admin/cli/ automated_backups.php
Does quickmail block need an update?
'spirit of sharing', Ken