Have I burnt out a component??? (no replies)

Hi Everyone
I'm new to the forum so please bare with me my terminology may not be great.
I have complete my first Prusa iteration 2 build. I wired everything up ran the test program, everything was working, great!
Now for some reason my Y axis motor will not run, regardless of what firmware or test program is used. All the rest work fine!!
I could really do with some help to identify or circumvent this problem.

What I have found:
- I checked all the wiring between the motor and the ramps(1.4), wiring is fine.
- I have used the same stepper driver (A4988 G3D) in different positions on the ramps board and it has operated (ie for different axis'), driver working.
- I have tested the motor, motor working.
- I have tried different variants of Firmware, firmware working.

So i reckon somewhere between my X-axis driver and the Arduino there must be an issue, anyone have any ideas?? Have I burnt out some component on the Ramps or maybe the Arduino

Also i have spare ports/pin array for a second extruder which works fine (E1 as labeled on the board) and i'm only using one extruder, i just don't know how and what numbers and lines to change in the firmware to make this the X-axis instead of a second extruder.

Any help would be greatly appreciated

Thanks
Alan