I am going to assume that you have a secondary parallel port since it is unlikely you have enough inputs to use a pendant with a single parallel port.
Pins that are always inputs (10, 11, 12, 13, and 15) should not be a problem and I recommend temporarily utilizing these if you are not getting your input signals.
The data pins (2 thru 9) can be used as input for the Port 2 in Mach3. Make sure that you have the box labeled "Pins 2-9 as inputs" checked in the "Port #2" box of Ports and Pins for Mach3.
It may be that some parallel port cards use unusual registers to control configuration and Mach3 may not be able to make pins 2 thru 9 be inputs on such a card. If you suspect this to be the case and you have a motherboard parallel port available, you can juggle the port addresses such that Mach3 uses the add on card as Port #1 for step and direction signals, and the motherboard port for your pendant. Then Mach3 should be able to control the input mode. Make sure that the port is configured as AT or PS2 style, or EPP mode in your bios. Plain PC parallel port mode does not allow 2 thru 9 to be inputs.
The add on parallel port card sold by PMDX does work with Mach3 for inputs on pins 2 thru 9.