Well, the input voltage is going to be cut down by the electronics, so if you only start with 9.6 volts, you'll get less voltage at full throttle on the motor. Also, remember that if you were supplying AC, you typically get a boost in the DC voltage available to the electronics as the filter caps charge to the peaks of the AC voltage.
Since I have no experience with battery operation, and also know nothing about the actual electronics in use, I can't really comment in detail on why the locomotives are obviously not getting as much voltage/power to the motors.
