Right, I don't have this problem anymore. Most likely the problem started with a bad CPS but after replacing it the problem didn't go away. I wish I had a solution for it but the problem went away when I removed the BT OBD ELM327 I was debugging with. I would assume that the OBD device 'locked' the ECU in a stupid state... no idea, just speculating.
I never had that problem since and the only thing different was the OBD not being connected to the car.