Ultimaker original X-axis not moving - possible electronics problem
I'm not sure I know exactly what is wrong or what steps you've taken so far, but it seems like your extruder motor is broken and you've narrowed the problem down to electronics.

If so, replacing the Arduino, motor, and driver leaves only the Ultimaker PCB as the source of the problem. I would suggest ordering another - but not until you've contacted Ultimaker with the problem you're outlining here.