If the machine actually moves this will just be a simple Mach setup problem. The E-stop was actually working and changing pin selection proved So I would guess the rest of pins are fine.? What you should have done is toggle the active Low. Mach was sensing the signal the wrong side so thinks the E-stops activated.

Not sure what you mean about resource tab showing the same settings has in Mach.? The only number in ports&pins that relates to the LPT is port address and that is only entered in one place on the first screen. From then on the only number in the other screens IE Inputs,Outputs etc that relates to the LPT is port number 1 or 2 depending if you set port 1 or 2 on frst screen with the LPT address.
With the limit switch( and all other I/O's) you will need to know the pin number from the BOB and enter that number in Port&Pins/Input signals/X++/x--/pin number do the same for each Axis.
Without the BOB pinout you will be stabbing in the dark.
After doing this check diagnostics screen and the M1++limit/2/3etc LEDs and if lit without switch tripped the toggle the Active Low again.

If you still struggle then post the make of the BOB and any pin info you may have I'll take a look for ya.