Hi,
I'm not a fan, and never have been, of using one switch as a Limit switch AND a Home switch.
My machine has dedicated Home switches, and where fitted, separate Limit switches, each on separate inputs.
The reason I prefer this is that when Mach is 'Homing' or 'Referencing' it treats Limit switch events as Home events, and in all
other operating modes it treats them as genuine Limit events and EStops as its supposed to. I suspect the reason that so many Mach users combine
Limit and Home in one switch is that was the practice which dates back to the Parallel Port which had so few inputs that you effectively had to combine
switches in creative ways. Nowadays with external motion controllers having many spare inputs there is no need to combine them, but the practice persists.
Your issue sounds like Mach is interpreting the switch event not as a Home event but a Limit event, even though its not supposed to.
May I suggest that you (in Ports and Pins) disable the Limit switch on that axis in the Inputs page but retain the switch as a Home switch only.
If you do this as an experiment it should prove whether Mach is mistakenly reacting to the switch event as a Limit. It may also suggest to you a solution.
Craig