We ran into a problem with course backups not deleting in Moodle 2.3.2. We have selected to keep only 1 backup. We saw bug report MDL-33531 and realized the issue started occurring once we had selected "include course shortname in backup."
To resolve it we upgraded to Moodle 2.6.2 as it seemed that backups had been significantly improved in the 2.6 version. The existing backups were still not being deleted when course backups ran. We deleted all backups, unchecked "include course shortname in backup" and let the backups run again. Backups are still not being deleted and curiously the course shortname is still included in the backup. We checked and the database clearly indicates no shortname is selected.
Has anyone run into a similar issue? We are out of ideas at this point. We will either need to turn off course backups entirely or schedule a time each week to delete the old backups before new backups run so they don't build up on the server.