A system to automatically calibrate gains and/or offsets for each position feedback signal in order to reduce variations between position feedback signals for each sensor in a linear drive system is disclosed. As a mover travels along a track segment, the segment controller records the position feedback signal output from each position sensor corresponding to a magnet on the mover passing the position sensor. The segment controller determines peak values for each position feedback signal and compares the peak values against a target peak value. The segment controller then adjusts a gain value for each sensor by a ratio of the target peak value to a measured peak value. The segment controller periodically monitors the position feedback values generated by one mover as it travels along the track segment and automatically updates the sensor gains as previously described.