[Al Skierkiewicz]

Zach,
What you are describing is likely caused by mounting screws that are too long for the FP motor. One of the screws may be touching the wiring inside the motor hence the 46 ohms you read to chassis. If you were to measure the resistance on an FP motor, you will likely find the same value. (turning the shaft will produce different resitance readings but one will be close.) You might have a solderless connector pushed onto the motor contacts that is "leaning" far enough to allow the connector to contact the frame of the motor. This is an illegal condition and is likely the source of interference with the other systems. The higher the main battery voltage, the worse it becomes is due to higher voltage available in the charged battery. ( i.e. more current into the frame) Remove the FP from it's mount and/or remove the wiring to the motor and see if your resistance reading goes away.
al