That sounds like a fairly typical EMC problem--either the rotating magnetic field or RF noise from the brushes (if present) is getting into the board + causing interference. Possible solutions (in order of complexity) might be:
-Move the controller away from the motor.
-Switch to a lower-noise motor.
-Shield the controller by placing it in a conductive, grounded box (a steel box is recommended due to its magnetic properties). Also, consider adding a ground plane to the controller board.
-Shield ALL lines going in or out of the controller and / or position them away from the motor--this includes power lines. Also, power lines should be filtered when they enter the controller board.
-Reposition the controller to minimize specific types of interference (ie, no pulsing B lines normal to the board).
-Harden the controller itself against interference by identifying / minimizing sensitive points. For example, signal lines should be low-impedance to minimize induced voltages.
-Get the device to an EMC lab and do a proper analysis on the noise output / susceptibility for all components. Use the results to make the appropriate modifications.
-Get a copy of Maxwell or some other EM simulator and do basically the same thing.