Please just take this clue:-
Dedicated Input Pins of ESS are
Pins 10, 11, 12, 13, and 15 of all 3 ports
They all are ACTIVE LOW meaning when there is a 2.5V to 5V on the pin is is NOT active. When pin is low 0-2.xV the the pin is active ie limit switch is triggered. So in MACH3, limit switches pin MUST be set ACTIVE LOW for sure.
But which pins?
If you know which pin is e-stop (say it is pin #15) then you can guess that X , Y, Z, A limit switch are pins 10, 11, 12, 13 respectively.
A bit of experiment while looking at the diagnostic page of MACH3 is all you need to do.
If on the diagnostic page a yellow light is on mean you must change to set the pin active low (instead of active HIGH now).
Reuel