An apparatus is provided for writing reference patterns on a data storage disk of a disk drive. The disk is rotated by a spindle motor. A back EMF sense circuit generates a sequence of zero crossing signals from back EMF sensed on windings of the spindle motor over each revolution of the spindle motor. The sequence of zero crossing signals define a corresponding sequence of zero crossing periods of time between successive zero crossing signals. A Phase Locked Loop (PLL) circuit generates a timing signal in response to comparison of a feedback signal to the zero crossing signals. The PLL circuit also compensates for repeatable variation among the sequence of zero crossing periods over each revolution of the spindle motor so that the timing signal is substantially independent of the repeatable variation among the sequence of zero crossing periods. A recording pattern generator writes reference patterns on the disk in response to the timing signal as the disk is rotated by the spindle motor. Related methods of making a disk drive are also provided.