I run Tuner on a regular basis. Tweaks have been needed from time to time ... and always upwards on sites that are used.
In the hashed directories that have backup.mbz files ... change into one and
head -n 40 moodle_backup.xml
That will show course name and ID. Go visit the course via Web.
Also what is destination for autobackups? Back info moodledata/filedir/ is default. I prefer those go to a designated directory manually created where I can count 'em and see 'em without having to mess with a DB query to see where they are in the maze or filedir.
If you have a designated directory ... is that an SSD device or a mount point to NFS or what? Could be a bottleneck.
No science to this issue ... just a lot of investigation ... scratching head ... trying something ...