I did not know he was using a SmoothStepper, these machines are normally basic Parallel port or USB and yes the Smooth Stepper has it's own Noise filtering ( Debounce )
How do I set up Noise Filtered (debounced) input signals?
Go to Mach3's Menu -> Plugin Control -> Main Config: ESS-M3-version
Noise Filtering of inputs (also know as debouncing) will help to eliminate random fluctuations due to noise, by requiring a consistently high input signal before changing the input state high or by requiring a consistently low input signal before changing the input state low. This is very useful in situations where there is a lot of noise that can corrupt signals (like a plasma system), especially for things like limit or home switches, probe signals, EStop, etc...
Enter values in microseconds (us) that a signal has to be stable for before it has been considered changed. Start with a value of 10 us, and work your way up through 50, 100, 250, 500 or possibly 1000 us (the same as 1 ms). Keep in mind, the higher you go the longer of a delay you are creating before your signal can get through, and this can cause a disaster while probing. If you have more than 100 us worth of noise, you should really look into your wiring and try to rewire or redesign your system to eliminate the noise sources or your wiring's susceptibility to noise.