A method of tuning a servo control system in a disk drive that implements seeks using a the feed-forward command effort signal uffwd and a PES reference signal r that were designed to be compatible with one another on the basis of a modeled frequency response G0(z) that is different from an actual frequency response G(z). The steps includes scaling the feed-forward command effort signal uffwd to substantially achieve a zero velocity condition at an end of the seek; scaling the feed-forward command effort signal uffwd to substantially achieve an on-target condition at the end of the seek; and modifying the PES reference signal r such that it substantially varies in unison with the indicated PES signal y during the seek