In Config you could test each pin as an Estop.  It would mean testing one by one. 

You may have a problem seeing the results in the on screen interface ( as I've had with the outputs - relays turning on/off with no display ) but it may in fact be reading it.  You could enter in the various pins as an E Stop and test them.  When input is triggered it will stop the program ( if working ).

It would take a while to work through them but it would ensure the BOB, cable, and input switches are all wired correctly and working properly.  Then it would be a matter of the type of card or how things are configured on the whole.

Here is what I found for port 2 for this particular PCI Card:
I will list the LS name, then the  BOB pin number (which is actually the DB25 pin #) and then the input pin number for the Mach3 for each input:
LS Name   Cable Pin    MACH 3 Input #
X ++,         15,                2;
X - -,          13,                3;
Y ++,         12,                4;
Y - -,          10,                5;
Z ++,          3,               13;
Z - -,           4,               12;
A ++,          5,               10;
A - -,           6,               11;
Input 1,     11,                 6.

I used the automatic switch setting to find out which was the true input # when I grounded a pin on the BOB.  I stopped caring about the LED's once I could determine which hardware input was related to which actual MACH 3 input.  

Resolved then?

Is it just an issue with the LED not displaying the state change?

No, the LED would display the change if I had guessed the right pin, but as you can see there is not a correlation between what my BOB pin #s were and the actual pin #s that the input to MACH 3 was seeing.  So using the auto detect function, I was able to determine the correlation as displayed in the table above.  Start auto detect, ground let say pin 11 on my BOB and auto detect would tell me that is really pin 6 for the input.  Stepping through each input gave me the relationships.  

One of the problems with not using auto detect is you can not tell which pin you are activating until you hit ok,  Auto Detect tells you immediately right on the input screen, and also changes the pin number for you, all you have to do is keep track of which pin on the BOB you activated and write it and the Auto Detect response down so you can then wire the dang thing. Thus the table.

I do not think this is normal and I should have been able to know that pin 11 on the BOB would activate pin 11 on the input. and if I put that in for INPUT #1, that LED should have lit.  I have a new PCI Printer port coming and a new BOB.  It will be interesting if this all straightens out to a one to one relationship or not.  Let you know next week after I get the parts.

I know I get wordy with my responses, but it is important that all details are available to anyone else having a problem as this may give them some insight.