A system automatically calibrates 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. 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 periodically monitors the position feedback values generated by one mover as it travels along the track segment and automatically updates the sensor gains as a function of a ratio of a target peak value to a measured peak value of the position feedback signal. The segment controller also records the position feedback signal from each sensor when no mover is traveling past the sensor. The segment controller periodically monitors the position feedback values received when no mover is present and automatically updates sensor offset values.