Compare \core\task\automated_backup_task with \core\task\backup_cleanup_task:
These course backups in /moodedata/temp/backup/ maybe failed because we ran out of space. At the moment I see only 4 directories, so other 8 courses was completed or was deleted automatically. For these 4 remaining courses only two had moodle_backup.xml file and checked these course, they had automated backups done last week. The other ones maybe had to be course backups but didn't started because run out of space? Just my guess...
Currently /moodledata/temp/backup/ is only ~300MB.
I would like to get back to /moodledata/trashdir/ then.. So now in Filezilla I see that it has 256 directories.
And this is the maximum directories size which can be as I understand.. 
And I am sure that these directories at 4-5AM for sure are not teachers who deleted something, so these are the oldest backups files from moodledata which was deleted because new was created. So even if this is old backup it will stay in trashdir for like 24hours or so?
Or if we would run our cron.php every minute it would get deleted much faster?
Also about which timeouts are you referring to?
Thanks,
Marius.