Its the motor brushes. The can motors we are using are not the same quality they once were. We use them at very low voltages, so the brush gear is more critical. If you can run the pump with a loop (fuel in it) at 2v for an hour, its to bed in the brushes more than the pump.
I use a 2v Glow Jelly battery or my Graupner charger that has a motor run in option for running brushed motors.