I may be off base here, but wonder if there is quite a difference between wiring the three limit switches in series, to one port, versus individual limit switch lines to three ports.
It would seem to me that if the three limit switches were in series, when you home the mill, the first switch to hit its limit would stop all axis movement toward home. This would result, for example, I think, if the Z axis limit opens first, the gantry stops with the X and Y no where near the home position.
If you wire the three switches to their own port, then the three axis will always go to the same home position, the place where the three switches go open as determined by the position of the limit switch stop block.
Just another thought about how to do it,
George