in your linuxcnc /configs/machinename folder
have you used stepconf to set the limit switches to the correct parrell port pin you wish to use
if possible post your hal file from your config setup
have you selected or jumpered the pullup resistors on the breakout board ?
are the switches connected between the approprate pin and ground on the breakout board ?
which probotix breakout board are you using their are a few types ?
limit switch wiring is shown here
www.probotix.com/manuals/PBX-2_manual.htm
their is also specific emc configuration information shown here
www.probotix.com/support/