There is an LED on the BOB for each input and output. Does the LED change state when you activate the limits? If it does, then you know the switches are working, and the optos on the BOB are working. If you're not seeing the "LEDs" in Mach change state, then the problem is the PP drivers on the BOB, or the PP itself. If the LEDs on the BOB do not change state when you activate the limits, then either the switches are not working, or are incorrectly wired, or the optos on the BOB are likely blown. You can order replacement opto chips from CNC4PC, or try swapping two of the opto chips on your board, to see if that gets the limits going. The opto chips are the LTV847s at positions IC5, IC6, and the chip between IC6 and the PP connector (which does not seem to have an IC designator....). I would guess IC6 is probably the one that is used for all the input signals.
Regards,
Ray L.