Does the unit work if you have only the USB port connected ie without any encoders or connections to M1 or M2?
The PC will earth the 0V on M1.25 and M2.25 and you will have huge stability problems if you connect 0v from these anywhere to ground.
You may get better responses from the CNC Brain forum at
http://www.safeguardrobotics.com/default.aspx?tab=forum where there are some people, like myself, with real machines under development.