my theory is, since these Hitachi throttle bodies are so sensitive to manual actuation of the flap even when disconnected from the car, the rush of pressurised air might be strong enough to move the flap just enough to make it think the ECU has lost control over the flap - as in the flap is moving beyond its intended position.
check your throttle maps too - run the stock one for a bit and see if the fault persists
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