Just looking at your photo's again - that LPT cable looks very small diameter so must be very small wires, try another cable and make sure that the shield / 25 way connector outer metal part does not connect to your machine ground. (this cable screen is connected to earth at the PC end)

Tweakie.

Not too sure on that one cause I changed ports even from the onboard lpt to the pci one I had installed and it gave me the exact same results.  It's not the cables cause I've changed them and I highly doubt that 3 different cables would have the exact same problem.  It's now left me with 2 possablities, it's either the bob or mach3.  When I first move an axis when mach3 is started it gives me really strange results untill it's been on for a couple of minutes, then it just gives me the same end result where my y won't move untill my x moves first.  My results when mach3 is in it's first minute have been posted here and as you can see it's never the same untill it has been on for a couple of minutes.

2 days with an automation tech here and still no further then I was when I originally installed everything.  One major problem is that we have 2 different pin settings, one from the company I bought this off of and one from Texas micro circuits.  They are a little different, but it seems like neither one is correct for the board.  I can go into pins and ports, and change nothing, but click ok and I get different responces from my axis then the time before.  some times one axis will control different 2 axis at once, until I play with them for a bit then they seem to work themselves out, but then I go back to my y not moving until my x moves. 

I'm almost ready to start bashing heads.

I am not meaning to be unkind but the wiring is not the best and I see no shielding at all, I would hazard a guess that noise is at least part of your issue.
Hood

I'm almost ready to start bashing heads.

So did you try bypassing the breakout board?  I went nuts for half a day trying to sort out weird behavior and then finally decided to bypass the BOB wiring directly to a DB25 shell and everything has worked beautifully since then. Needless to say I have a low opinion of BOB's.

Chris  

Where would I be getting the noise from?  The plasma's breaker is still shut off.

Where would I be getting the noise from?  The plasma's breaker is still shut off.

Electrical noise is everywhere, PC, strip lights, fan, even from your neighbours on your incoming mains supply. 

Seriously though, good routing of wires and shielded cables really pays off in the long run.

Tweakie.

Ok but this is the last time I'm rewiring this pos. 

The power supply for a start.
Hood

You have to be cunning when it comes to avoiding electrical noise problems and probably the single most common source comes from wiring loops. Loops act as antennas and pick up anything, especially if it is not required (Murphy's Law).
Avoid Earth Loops and avoid GND Loops.
Treat Earth and GND as two separate circuits.
Only terminate the shield of cables at the controller end and preferably to one single point.
The list goes on....

Tweakie.