Hey Varun,
I think Brian was on the right track when he mentioned the possibility of exceeding the common mode voltage rating. If I understand your circuit, your controller is essentially providing a potential which is divided across the motor and the resistor. The common mode voltage for this card is 12V, which means that the difference from the lowest potential of a measurement to the highest potential of a second measurement cannot exceed 12V (with respect to the same ground).
Be sure that you're not exceeding the common mode voltage by checking the voltage output from the controller. I may have misunderstood your circuit, so if this doesn't solve your problem, please attach a diagram and we'll take it from there! (to attach diagrams, check out the forum help)
Happy new year!
Elijah Kerry
NI Director, Software Community