So Ive got my machine pretty well all set up, everything seams to work as it should, limits all activate the LEDs in Mach when tripped and stop motion in that direction while allowing movement back off the limit switch under command or jog. On the Galil side, quires to the limit switches all show the correct state for either normal or tripped.

The problem is when trying to home the axises. Pushing the "Home All" button will cause the Z axis to run to the top and trip the limit but then it just stops and does not pull back off the limit. Galil shows the limit as tripped, but the LED in Mach will not indicate a tripped limit until resetting Mach. Once reset you can use jog to back off the limit without any problem. I get the same result with the other axises if I try and home the axises independently from the diagnostics page.

Im using the limit switches as homes, and have the "use limits as homes" box checked in the settings, and have the input pins set up as per the plugin manual. I have also tried debounce settings up to 20K without any luck, and the switches are new. The limit switch wires are all shielded and run well away from any other wiring so I dont think it is noise.

I suspect that it is just a setting somewhere, or something simple that I am overlooking but Ive run out of ideas as to what.  

Found it. It was as I expected something simple. I did not have jumpers from the limit inputs to the home inputs. Couple short pieces of wire and it all works now. Time to make some chips.