Try a new install and add NFS mounts and hold off on all that SB/CP junk and see if you get the same result.
Not really looking forward to that, but might be the only option.
Install an Ubuntu VM to see if I can fsck the SD-card.
Did a check on the SD-card.
Turned out there was a “dirty bit”, which I apparently repaired.
Let’s find out if that fixed the issue!