So finally
Removed the debounce from Mach3
Changed the debounce in SS from 500 us to 10 us.
Added four 0.1 uf caps to each of the inputs.
The system is able to home correctly on all 3 axis.
One small thing that would have really helped, if the limits lights on the diagnostic page were sticky. That is, once its set, it remains set until its cleared.
A small momentary noise spike will trigger the limit, but there is no visual indication on the panel that such an event has occurred . That kept me wondering as to what the problem could be.