If I'm thinking about this correctly, the potential energy in the fuel isn't changing the net kinetic energy of the total mass, it's just re-distributing it between the vehicle and the exhaust.
Total momentum is conserved, but distributed: the individual momentum of the vehicle and the exhaust jet will be of equal magnitude and opposite direction (assuming a straight line), so if the rocket started in free space at rest (zero momentum), after it's run for a while the exhaust jet and vehicle will have equal and opposite momentum vectors.
Energy is a different thing, but related to specific impulse. In a perfectly efficient system (not what really happens), the decrease in stored energy within the fuel tanks would be equal to the increase in total kinetic energy (i.e. the sum of vehicle and exhaust kinetic energy).
