If you disconnect the NI 9243, can you power the motor normally? Could you post a schematic of what you are working on? Have you measured the voltage at the connections to the motor?
With the NI 9423 disconnected, the motor works normally. I attached an oscilloscope to see the pwm signal. With no 9423 connected, the signal had a 12 volts peak to peak. Then when I attached the 9423, the pwm signal going to the motor dropped to about 1 volt peak to peak. However, the 9423 was reading a 12 volt peak to peak signal.
Could you give me a schematic and also more information about why you have it wired up this way. I don't think I quite understand how it's wired up from your description.
Also, here is a document about the current and voltage characteristics of the 9423
The different current draws of your two devices may be the source of the problem. Have you been measuring current?