A compression ignition engine is fueled from common rail fuel injectors that predominately inject natural gas fuel that is compression ignited with a small pilot injection of liquid diesel fuel. Before and after a rapid fueling increase transient, the liquid and gaseous rail pressures are controlled toward respective pressures based upon engine speed and load. During the transient, the liquid rail pressure is controlled toward an elevated liquid pressure in order to cause a surge in the supply of gaseous fuel to the gaseous fuel common rail to proactively satisfy the increased gaseous fuel injection rate while obviating a substantial pressure deficit in the gaseous fuel common rail.