Well, I found out the problem why my gantry limit switches were shorting out.
I caught sight of some sparks in the homing sequence early this morning when there was not much light around. One of the wires on my lower z axis limit switch was being caught on the bearing support.
image missing http://i210.photobucket.com/albums/bb270/rodweb/Mobile%20Uploads/2017-01/20170128_103942_zpshim40mzi.jpg
I have known for a while I needed to swap the microswitch with the trigger so the wiring was never moving.
image missing http://i210.photobucket.com/albums/bb270/rodweb/Mobile%20Uploads/2017-01/20170128_104009_zpsl1ky4mpo.jpg
I had put it off becasue I wanted to get something moving! Looks like I'll be doing it sooner than later...
I've also found a bug in gmocappy GUI when Joint Axis machines are in use which I reported on this thread
forum.linuxcnc.org/gmoccapy/32227-bug-re...mode-in-master#86816
Gmocappy allows individual homing of a joint. Before we had the new Joint Axis feature in LCNC, the joints mapped directly to an Axis
image missing http://i210.photobucket.com/albums/bb270/rodweb/Lathe/Plasma/Screenshot%20at%202017-01-28%20111329_zpsbegzrrus.png
So the buttons at the bottom of the screen above are meant to HOME ALL, HOME X, HOME Y and HOME Z.
But in reality they act as follows: HOME ALL, HOME JOINT 0, HOME JOINT 1, HOME JOINT 2
In my setup, JOINT 0 and JOINT 1 are paired together to operate the X axis. This means that
HOME X and HOME Y buttons are homing opposite sides of the gantry. Only the stepper on one side runs. This is a bit scary if one is selected in error as it will twist the gantry.
Then everything is out of step so HOME Z homes the Y axis and the poor old Z axis misses out altogether.
From what I can see, There is no way to home an axis on its own, only a joint and home all.. So I need to disable the individual homing buttons somehow. Preferably without editing the main Gmocappy source files as my changes would get overwritten on an upgrade.