. I now need to swot up on the full details of G54, G55 and other relevant codes and exactly how LinuxCNC uses and saves them.
Yes this confuses many people. Have you noticed that you can see the machine coordinates and the current G54,55 etc on some GUIs at the same time. In Linuxcnc you can turn them on and off from the view tab.

Ie. If you have touched off your part ie X0,Y0 in G54 you will see the machine G53 at the same time completely different.

http://linuxcnc.org/docs/2.8/html/gc...es/offsets.png

http://linuxcnc.org/docs/2.8/html/gc...ordinates.html