The disclosure describes an engine system having liquid and gaseous fuel systems, each of which injects fuel directly into an engine cylinder. A controller controls the pumping of a liquefied natural gas (LNG) in the gaseous fuel system using variable speeds for reciprocally moving a pumping piston of a pumping element with a drive assembly. The controller adjustably controls the drive assembly of the pump system to vary a time period for the pump cycle based upon a comparison of a pressure measured in the accumulator and a target pressure condition. When the accumulator pressure satisfies the target pressure condition, the controller is adapted to control the drive assembly such that the pumping element is in a creep mode in which the pumping piston continues to move, but produces no more than a nominal amount of compressed LNG.