A system and method for monitoring disturbance forces experienced by a mover in an independent cart system monitors current generated by a controller and a feedback signal corresponding to operation of the mover in response to the current generated by the controller. The controller stores a value of the current reference and of the feedback signal, sampled in tandem, and determines a disturbance force experienced by the mover as it travels along the track as a function of the stored values of the current reference and of the feedback signal. The controller may store the measured disturbance force experienced by the mover as a function of the location of the mover along the track. For each subsequent time the mover travels along the same length of track, the controller may add a compensation value to the current reference to reduce the disturbance force experienced by the mover.