We had that same problem, and based on your description, it sounds like you are using a case structure. Rather than using a case structure, I would use
this as an example. I originally used a case structure and had a similar problem. I hope this helps, but if it doesn't or you aren't using NI Labview, sorry.
You can also use the throttle on one of the joysticks to control the motor, but it can be a little touchy, so I would recommend using the above link.