Parallel Port failure?

My setup uses 3 parallel ports, one on the mother board, and the other two provided by a PCI card. The system has been performing flawlessly for a number of years. Recently it has failed and I have not been able to determine what the cause is.
Using Hal show to see what the parallel outputs are, I find they do not agree with what I see on the Axis presentation.
For example when Axis starts the Axis screen shows as it should that "Machine on" has not been actuated. Looking at Show Hal configuration under Pins/parport/2/pin 2 it shows red (no signal) which agrees with the axis display.
Yet when I look at my breakout strip for port2 pin 2 I have a signal present.
Checking my hal file I see the statement:
net machineon halui.machine.is-on parport.2.pin-02-out
Assuming the PCI parallel port card had failed, I replaced it with an identical one and still get the same results.
Can anyone give me a clue as to how to resolve this problem?
jensor

This is certainly a hard question.

If you can try another pc with the same hard drive and 2 external pci card's. I would give it a try first. Good luck !!
Jensor suggests nothing is changed at the software side.

These files were created with Gedit. I added a .doc suffix assuming that would be okay. Gedit should open them for you.

Ok, I renamed the files by changing the suffix from .doc to .txt. See if that works for you.
Thanks
jensor

Thanks for the help. I am in the process of setting up another computer. Need to jump through a lot of hoops. Its been so long from the last install.