Robert W.: A while back, when Lionel Trains were still MADE IN AMERICA, there was a problem within the pullmore motored F-3 diesels. While your description of what is happening is not entirely clear; you may want to try these helpful fixes.
At one time, the driver/receiver board was mounted over the fuel tank at the sill height of the frame. This placed the receiver section of the board right next to the rear pullmore motor stator field. The eddie currents of the field caused some difficulties with the reception/processing of the signals sent to the unit. One fix was to lower the receiver/driver board deeper into the fuel tank, to get it further away from the motor field. Some of the driver/receiver boards were supported by a tall plastic stanchion at one end and there was a multipule holed heatsink at the other with the board mounted in the upper holes with nut and bolt. You can unbolt and lower the driver/receiver in the heatsink and shorten the plastic stanchion at the other end. This will move the receiver further from the offending range of the motor.
If this does not help or has already been done by the factory, then an additional item can be added. A small tin L-shaped shield is mounted at the rear edge of the fuel tank at the sill level between the motor and the receiver/driver board. You will see an opening for a switch with two screw holes that can be used to attach the shield. You only need a small lip to mount it, but it should extend up about 1" high. This will help shield the receiver from interference from the motor field. These were factory designed fixes for those who experienced difficulty controlling their diesel.
Again, as was stated by others before, proper lubrication and a good run-in period will always help the pullmore motored diesel perform better. Hope this helps. Dennis M.