Not sure I can help much, I'm afraid, but I would consider unloading all plugins then killing off the rig npcs and letting them respawn again, to see if the issue comes up.If not, you can attribute it to some plugin and start the process of elimination.
I'm sure there's a default command to force-repopulate the Oilrig...Can't remember, but I left a command 'repop' in CustomLoot for testing/debugging.
CustomLoot does absolutely nothing to loot until configured so, if it makes things quicker, you could install it and use that `repop` console command to speed up your testing.