If it isn't doing scan to mailbox (hdd is filling over time because they don't delete the jobs when done) then there are only 2 options
The Fix and the stop gap.
Fix = Altboot no data backup no clone to latest firmware
This is not a Connectkey known issue on any firmware, so the issue is this machine specific, corruption or a hardware failure. Corruption can't survive this process, but of course you will have to set up everything all over again from scratch.
Stop gap = Set the mailboxes to delete files older than x amount of days, and set Secure disk image overwrite to happen daily when nobody is there.
That would normally be a valid suggestion but the issue occurs before any attempt at scanning.
It would appear to be a situation that builds up over a period of time.
Sounds like the scans are quite simply too large to stay in memory, I would assume a very large build job or you are using very high DPI and very little compression , which is causing massive file sizes during file creation and filling the available memory on the device.
Depending on the job in question, it could be fixed by breaking up the job a bit, or even simply using the TEXT preset (Whitespace is not counted as data in the filing)