Odd,
When you did they swap, did you also swap over the Engine Cooling Fan ECU? Although they look identical, there not!
The Gen II Cooling fan operates completely independent of the Engine ECU.
In the Gen III, the Engine ECU has an override wire, so it can operate the cooling fan, independent of the Engine Bay Temp sensor.
The car will still work with either of the Cooling Fan ECU's. I've done a Gen II 3sgte to Gen III 3sgte swap and the only Pin I had to changeover was the relay for the Fuel pump. I also had to Ground one of the Engine ECU pins to stop it thinking it was under high electrical loads (Defogger ON or headlights ON) and raising the idle speed.
Being that you came from a NA, there may be more re-pinning required.