It should work regardless of whether the axis home and limit are the same switch / pins.
I am not sure what is causing your error; however, Mach 4 is not the problem with using home and limits on the same pin. There must be something else wrong with your settings.
I have an AVID CNC that came with Mach3 and its home and limit switches are the same switch for each axis. I upgraded it to Mach4; and, I never had a problem like this.