Unstable PWM from DI/O pins from sbrio 9636

Hey guys
Im trying to control a Vex Motor Using a PWM generator VI in the FPGA of the sbrio 9636, and I output this signal to Pin 5 of the Digital I/O Pin. Our PWM parameters are 5% duty cycle with a frequency of 50Hz. The output of the PWM is very clean, but its very unstable as the duty cycle changes substantially and the signal itself flickers on and off when measured through an oscilloscope. I've used this signal to drive a vex motor but the motor does not drive well at all. I know its not the motor controller and the motor itself  as I have inputted a pwm signal from a waveform generator with the same parameters and the motor runs smoothly. Is there a way to make the PWM output from the sbrio more stable ?
Thanks

the problem is with your code but you did not post the code.
Stu McFarlane
Viewpoint Systems, Inc.

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