I hate to say it, and I might be wrong... but it sounds like you've somehow fried it. The most probable cause, is the power was inadvertently turned on while the motor was in the stowed position... and is the reason you should unplug it after every use. I went one step further and installed a 50 amp circuit breaker between the battery and my motor, now i just flick the little switch and all power is killed to the trolling moter... lots easier than jiggling the plug in and out.
I hope this helps.