Interesting. Ok I've had problems with the limits tripping on this router due to vibration, best guess, every once in a while. It hasn't done it in years. Could be bad switches, but the X Switch definitely worked for referencing then when it backed off it didn't back off enough to reset the switch. I know because I push on the switch lever and it didn't click.
So assuming Mach works the way you explained then I'll see if I can find the root problem, I don't want to mask it with my Pokeys software.
I already had the machine setup for the X- and Y- for limits and home when I was running Mach 3, I don't see any need to change it now.
Thanks for the help.