There is provided a method and a control scheme to control an internal combustion engine operating in an auto-ignition mode by selectively activating a control scheme for controlling fuel injector operation based upon engine combustion parameters, e.g., IMEP or NMEP. The method comprises operating the engine in the auto-ignition combustion mode, and monitoring combustion in each of the cylinders. The fuel correction is selectively enabled only when either one of a partial burn and a misfire of a cylinder charge in one of the cylinders has been detected.