Interesting...
I'm guessing you didn't try shutting it down with the mag switch when the engine it was 'standard'?
Does the system retain the standard injector manifold (the 'spider' with the injector tube 'legs')? You say 'pumps' plural. What pumps are they?
On a standard injected engine at idle, switching the mags off will usually result in a reduction of RPM that reduces the fuel pressure out of the FCU and a consequent shutting off of the valve in the injector manifold and, therefore, no more go juice to the cylinders. Maybe the pressure out of the new pump/s(?) remains quite high in the FlyEFII system.