A print engine controller for a pagewidth inkjet printhead having a plurality of abutting printhead modules mounted on a carrier. The print engine controller is configured to: (a) receive data identifying a rotational yaw displacement of an erroneously displaced printhead module; (b) determine a correction factor that compensates for ink dot displacement by nozzles in the erroneously displaced printhead module; (c) use the correction factor to determine an accumulative Y-offset for each printhead module in the printhead; and (d) alter the output of the ink dots from nozzles in each printhead module having a non-zero accumulative Y-offset to compensate for the rotational yaw displacement of the erroneously displaced printhead module.