A printing system includes a pair of encoders to compensate for encoder noise in the velocity of a media transport as the transport moves past a plurality of printheads. One encoder monitors a roller that positioned at a location of low thermal stress and the signal generated by this encoder is used by a controller to maintain a constant velocity for the media transport. The second encoder monitors a roller used to drive the media transport and is positioned close to the print zone opposite the printheads. The signal from the second encoder is used to identify a corrected distance between each tic in the tics generated by the second encoder and the corrected distance is used to count a firing distance for generation of a dot clock signal to activate ejectors in a printhead when a substrate has traveled the firing distance.