When two fuel shots such as the main and anchor fuel shots are closely coupled, the controller is operable to determine a total main and anchor fuel quantity, a main shot duration, and anchor delay. The total main and anchor fuel quantity is determined by subtracting a pilot shot fuel amount from the governor fuel output, and a sensor senses a rail pressure. If a triggering condition is met, preferably a main shot fuel amount being less than or equal to a minimum main shot fuel amount, the anchor duration is determined from a map using the main shot duration, anchor delay, rail pressure, and total main and anchor fuel quantity as factors for setting the anchor duration.