Two weeks! Wow! Do hope you enjoyed your time away!
Anyhoo ... when automated backups are successful there are no directories left in moodledata/temp/backup/. Only 0 byte .log files.
Cron job/task for cleaning up temp area should be executing to remove any un-finished backups/failed backups ... no directories should remain. Ownerships/permissions? Know you've probably checked and double checked that but it could be related.
Are you seeing any errors in web service logs like can't unlink? (that's removing/deleting something).
You appear to be dealing with a site larger than I've admin'd before, so can only share what I did to address the same problem on a smaller site but with very large courses ... 100+ gigs.
Didn't use Automated backups. Had to create my own little bash shell scripts that used the CLI scripts for individual course backups and those were cron'd. I first had to find which courses were the largest ... used moosh to give me a ball park estimate of file storage for a course. Then used looping bash shell scripts ... one for large, one for medium, and one for all the rest that were cron'd to run at different times all pointed to saving the backup to a directory outside of moodledata. Didn't do both. Makes no diff however in that moodledata/temp/backup/ is still the directory used to build the backups. No option in Moodle config to change that location.
The large cron/courses set to execute Sat. at midnight ... might finish by Sunday morning.
The problem you will have in reporting this to tracker for someone to look at ... steps to replicate ... and whoever looked into it would have to have a site pretty much equal to yours. :\
'spirit of sharing', Ken