A first registration mark is printed by a first printhead on print media at a first initial encoder value. A second registration mark is printed by a second printhead on print media at a second initial encoder value. The second registration mark is spaced apart from the first registration mark. The first and second registration marks are detected using the mark detection system as each is transported past the mark detection system. The displacement signal is used to measure a displacement of the print media between the detection of the second and first registration marks by the mark detection system. A cue delay value is determined for the second printhead so that a subsequently printed first image plane and a second image plane are registered relative to each other using the displacement, the first initial encoder value, and the second initial encoder value.