The failure of the pilot to correctly set a new transponder code and an anomaly in ATC software that precluded the controller from manually overriding the resulting inhibition of displayed data. Factors in the accident were impaired function of the collision avoidance system in the other airplane due to structural masking of the airplane's transponder antenna, an intermittent failure of the approach controller's communication radio transmitter which interfered with his ability to communicate traffic information to the flight crew of other airplane, the failure of both the approach controller and the tower controller to issue safety alerts when the traffic conflict became apparent, and the failure of the flight crew of the other airplane to maintain an adequate visual lookout to see and avoid the airplane.