may be You have a EMF (elect.magnetic field)-problem. It means that the motor is working as a transmitter becaus of any defect in it. Is this a brush motor?

The encoder cable have a function as a sensor to if it is not grounded in a correct form. First I suggest to use an radio receiver in the near of the motor an check out all frequencies to hear some sound of the motor.

If You change the speed of the motor then You should have a change in the voice of the radio or a change of the amplitude or frequency on the scope.

Are You able to trigger the noise on the scope?

Are You shure that You have not still a ground loop?

regards
Werner