Look at page 5-22 of the manual. It may be what you're looking for.
Specifically, the "Home Sw. Safety" about mid page.
Home Sw Safety, if checked, will prevent motion of a axis during homing if the home switch is already active. This is useful to prevent mechanical damage on a machine which shares limit switches at both ends of an axis with Home.
Also, do you have your table limits set up and turned on within Mach3?