That is because you let Mach fix it and it set the active state of the limits and E-Stop to active Low, change them back to the way they were.
Which end of the cable did you disconnect? If the computer end then it would seem your parallel port is bad. To test change the port number for port 1 to  0278 and port 2 to 0378 and see what happens
Hood

I change the active low back (red X for all except the Estop) and now I have LED’s ON in the diagnostic screen for Y,Z,A but non on X

I unplugged the parallel port from the BOB and therefore I did not change the ports as you suggested. Let me know if you want me to do that

Unplug from the computer and see if the LEDs now light up on X.
If they dont then change the addresses and see what happens.
Hood

Unplugging the parallel cable from the computer did not change anything

The parallel cable is unplugged now from both the control box and computer

Changed the ports as you said and reboot Mach, now I have no LED's on X and Z. The LED's remained on Y and A

Can you attach your new xml and I will see if I can find an issue.
Hood

Sorry wasting your time Hood

Here is the XML

Ok it seems fine here. This is a pic of what I see when I load to this computer and as yo can see the LEDs match up exactly as you have the switches set in Ports and Pins, Inputs. If you are not seeing that then it would seem your computer is playing up, why I have no idea. Do you have a spare computer you can load Mach and then your xml and see if it looks like my screenshots.
Hood

Why you say it looks fine Hood? I have the same screens as you have with no LED on X and Z axes and I thought that we were trying to find out why I get no LED under the X axis

I have a laptop and another desktop in my office both with no parallel port. I can load Mach in either of them but I dont see what this will prove.

Another thing came to my mind is that I know when there are no LED ON in the diagnostic screen after you load Mach, all supposed to be fine and that is what I had when all inputs to the BOB were connected.

Anyway tell me what you want me to do and what we are looking for and no problem I will do it

M1++ is X++ limit, that is shown on LED and in your ports and pins so why do you say you dont have it and at the same time say the screen is the same?
Hood

Does this make more sense?
Hood