A control system includes a difference generating module for a rotating storage system that generates a position error signal based on a target position signal and a current position signal. A control module of the control system generates an output response based on the position error signal. A noise equalizer module of the control system generates a noise equalization signal that is based on a sensor signal, the output response and the position error signal. A compensation module of the control system adjusts at least one of the current position signal, the position error signal, and the output response based on the noise equalization signal.