mine did this on my mx5 and it was due to when i was fitting it. i had dislodged the sensor further up the pipework when i disconnected the airbox to connect the cone filter. check all the sensors and cabling are fully connected.
if that doesnt work try reconnecting your old airbox and see if you have the same problem.
the tube that connects at the back of the airbox what you connected the induction kit to, approx 10" up the pipe should be a sensor, check that mate. but it is a bit odd that it works ok when you connect the original airbox.
if your original box works then you pipercross must work.. make sure that the black pipe is connected to the sensor and the other bit of the sensor is connected to the induction kit try that mate it definately shouldnt be giving you problems..