Let the fun begin !!! ???

[JAZZCNC]

The relevant leds are on , on the BOB, my ports and pins are set correctly( they stop the M/C when triggered). but they only trigger briefly on the diagnostic tab. how are yours set up?

Don't worry about the Diagnostics Led's. It's working as it should and thats all that matters.
External motion control cards take certain duty's away from Mach3 and do it there way. This is why your motors drop out when limits are pressed. PLCM as taken over the duty's of watching the Inputs and won't be reporting this back to Mach constantly. You may find the PLCM software as some way to identify any active I/O.
Homing is another area that the controller takes over doing so don't be surprised if it doesn't work like Mach3 manual says it should. Mach3 by default assumes your using the parallel port which is completly different kettle of fish.

So long as the machine goes where it's told and behaves it self then don't fret if it does some things different to how Mach normally does it. You'll often find external motion controllers do it better anyway.