Most newer manual ECU's have different ignition timing.
Auto's decrease the amount of ignition timing when gearshifts are approaching, during and just after them to give the auto an easier life.
The auto g/b ecu interfaces to the engine ecu informing it when the gearbox is going to shift so it will decrease the timing. If it can't see the auto or auto ecu it will retard the timing constantly as if it is always in the middle of a gear shift.