Trolling Motor Blues . . .

I have a 96 Nitro 896 DC with a 50 lb MotorGuide trolling motor. I have a slight problem (especially on windy days). The trolling motor only runs at 12 V even if the switch on the foot pedal is set at 24 V! I have checked the batteries and resettable fuses, all okay. On weird occurence, when I unhook one battery, the trolling motor will only run on the 12 V setting. When I hook it back up and unhook the other battery, it will only run on the 24 V setting and give up 12 V. So, my question is, what the heck is going on? I think it might be the switch in the foot pedal or maybe something more serious in the trolling motor itself. I appreciate the help ;D