Hi,
When you take a look at the machine, remember to only be concerned with the color (red, yellow, green, blue) of the cable, as your logical X, Y Z, and A are only really significant to your software use. The way the drive box "thinks" about it is:
Pins 2 & 3 - RED
Pins 4 & 5 - YELLOW
Pins 6 & 7 - GREEN
Pins 8 & 9 - BLUE
You could set up the software "X" axis to use pins 1 and 14, in which case the drive box would not respond at all, and the software would think everything is just fine, and still show numbers changing on the screen and drawing pictures on the graphics screen like everything was OK.
Unless there is an overheat condition, the axes usually either work, or they don't work (assuming the motor cables and parallel port cables are all firmly seated and good). Thus, if you were able to cut the first pass fine, then the box would appear to be running fine as far as driving the motors is concerned. Things like backlash compensation, or trying to go too fast a speed, or accelerating too fast can only be fixed by changing the software parameters or changing the machine to have less weight or friction, or taking lighter passes with a sharper tool, etc..
If you need to send the box in, please contact me through e-mail. Go to the "Contact Us" link on the left hand side of the Xylotex web page for the e-mail address.
Jeff