Calibration system for multi-printhead ink systems

A method for calibrating a multi-printhead printing system, the method includes the steps of employing an encoder to track movement of a media through the printing system; providing a first printhead that prints a first image plane that includes a first test mark at a first defined location on the media as the media moves relative to the first printhead; providing a second printhead that prints a second image plane that includes a second test mark at a second defined location on the media as the media moves relative to the second printhead; employing a first image capture device that captures an image that includes both the first and second test marks; determining an error factor based on the placement of the second mark relative to the first mark in the captured image; and creating a frequency-shifted pulse train of the encoder in which the frequency shift is based on the error factor; wherein the first printhead prints the first image plane in response to output of the encoder and the second printhead prints the second image plane in response to the frequency-shifted pulse train of the encoder.