Often motor controllers have a potentiometer failure-detection circuit for safety:
This means that trying to replace the potentiometer with just an anlog output (low-pass-filtered PWM) won't work - you have to also replace the pot with a suitable resistor, and also drive the wiper connection with analog. Controllers commonly assume that if the pot stops taking a suitable amount of current then the controller should shutdown as something has gone open-circuit or shorted and the wiper voltage is giving an erroneous reading...