I think you have NATS if you have the red bit on your key for the car, or the blinking light on the dash? correct me if im wrong.
If your spare ECU has NATS Im not sure i it will work.
As for your problem, maybe water is getting in somewhere and causesing the problem, have you tried looking for water in and around the ECU area? IIRC pollyp had that problem when it rains...
