looking at the diagrams it looks like it could be the earths feeding the switches.
as you probably know all the switches use earths (negative) to do all the switching back to the controller the only positive cables are to supply lights ,motors and heaters , looking at gen1 the mirror switch and fuel flap switch share an earth, but gen 2 this earth also feeds the locking switch, so even though you've done all the swaps from the switches into the controller, i think your going to be missing some extra earth wires, so yes either change the loom, or check the diagram for pins that should have a cable and don't in your connector these will be earth wires feeding switches.