A disk drive is disclosed comprising a disk and a head actuated over the disk, wherein the disk comprises a plurality of spiral tracks, each comprising a high frequency signal interrupted by a sync mark at a sync mark interval. The head is used to read a spiral track to generate a spiral track crossing signal g(x.sub.n), where x.sub.n is a time in a demodulation window. A position error signal (PES) is determined in response to g(x.sub.n), and a deviation index is computed by correlating g(x.sub.n) with a nominal track crossing signal shifted by the PES. When the deviation index is less than a threshold, the PES is used to servo the head over the disk.