I have not worked with the NI MAX for a while, but I think it is possible to disable all limit and home switches somewhere in the setup for the axis in question. Also, it is possible to change the limit switch inputs from active high to active low and vice-versa. Depending on the type and wiring of limit/home switches you are using you have to set them to proper "polarity", otherwise they may seem active while they actually are not activated.
