A heating, ventilation and air conditioning (HVAC) controller, a method of receiving signals from a keypad and an HVAC system incorporating the controller or the method. In one embodiment, the HVAC controller includes: (1) a keypad having at least first and second banks, (2) a reference signal source configured to generate a time-varying untransformed reference signal and provide the untransformed reference signal to the first bank, (3) transformation circuitry configured to transform the untransformed reference signal into a transformed reference signal and provide the transformed reference signal to the second bank and (4) a processor having interrupt pins coupled to corresponding keys of both the first and second banks and a further interrupt pin coupled to receive one of the untransformed and transformed reference signal.