Well i think i have ruled out mechanical or errant pulses from the PC. I jogged both axis from the front panel today and both motors were audibly " glitching " so i took the motor off of the X axis and jogged it whilst not connected to the screw and it can clearly be heard glitching / stuttering. My guess is that its the driver board or main board thats gone.
I will msg Boxford but im not holding out a lot of hope, they will just say send it for replacement boards and that aint going to be happening, not at their prices :(