Argh, good progress, getting tuning right and then with the limits / home switches I was doing some test. I ended up somehow going past the X ++ endstop which has fortunately only cost me lost time as I now need to repack the ballnut and some of the cart bearings. Could have been a lot worse. Not sure why it ignored the limit switch.

I was setting the X and Y axis to be reversed as they are the wrong way around ( + and - direction ). Do people normally do it on Mach 3 or reverse either the -10 to 10V or swap motor leads (and encoder feedback)?