Embodiments of the invention include data storage system with a servo system with a VGA feedback loop that corrects gain errors for servo bursts arising from track phase misalignment and difference in frequencies between AGC and servo bursts for seamed and seamless servo patterns. After the servo fields have been written as part of the manufacturing process, in one embodiment measurements of phase misalignment are made and recorded in nonvolatile memory for use during normal operation of the drive. One embodiment includes measuring misalignment using relative signal magnitudes from test bursts with various linear densities written in a data area during the self-servo writing process. In an alternative embodiment the measurements of phase misalignment can be made real-time during normal operation of the drive.