It's steps per inch.  I also checked the x axis to see if an inch on the DRO's was an inch on the table and it was correct.

Grasping at straws here now.

Have you tried changing the state of the step pin active high / active low in motor outputs ?

There is another issue which keeps causing problems mainly with new computers in that some parallel ports now output 3.3Volts TTL instead of the old standard 5Volts TTL. Some driver circuits / boards will not work reliably with 3.3Volt TTL and some will just not work at all.
If you have a voltmeter then it may be an idea to measure the voltage on a direction pin whilst jogging the axis in one direction then in the other. This voltage should be approx 5V in one direction and approx 0V in the other direction. The voltage on step pins cannot be measured in this way only the voltage on a direction pin.
If  you find the voltage to be approx 3.3V this could explain why the setup worked OK with your old computer but now does not work well.
The easiest solution would be to fit a PCI parallel port card (assuming you have a free PCI slot) which does output the full 5Volts TTL signals.


Tweakie.

Man,  I really appreciate your input here Tweakie, I did try changing the active high/low.  Are all those settings contained in the .xml file?  If they are and it worked correctly before I rebuilt the computer... I am now wondering if maybe the controller got damaged or something? I moved it around a few times while remodeling my garage.
Or...
Is it possible the bios settings are different now? I went in and changed the bios setting for the parallel port from EES? to the recommended setting I found online which was ECP/EEC or something like that.  Sorry, I am at work right now cant actually look at the settings. Anyway, when I changed the setting there was a huge delay between key commands and movement of the motors and the stepper behaved the same way so I changed it back.  There were like four options for that setting in the bios.

The printer port LPT should be set to ECP.

I updated my earlier post to add more info.

Tweakie.

Cool,
I'll check tha whenI get home.  I don't really know which wires to check though.  Do you have a schematic that shows which pins to check? Would I be able to check that output voltage on the manufacturers literature for the Motherboard?

So, I checked the pins with the multi tester...
With the probes in pins 1 and 5 the voltage jumps up to 8.9v and stays there when I let off the up arrow when I press the down arrow the voltage drops to zero.
With the probes in pins 1 and 4 the voltage reads 3.7 when pressing the up arrow and returns to zero when I let off of the key, works the same way when I press the down arrow.
This is with the Sherline 1/2 Pulse option selected.  Without it selected I get zero on pins 1 and 4 when pressing keys.

Oh, now the x axis is behaving the same way.
Z still works.

When measuring the port pins - pins 18 to 25 are ground so the multimeter negative lead should be connected to one of these pins then the positive lead to a direction pin (generally from the group pins 2 to 9)

Don't know if this helps.

Tweakie.

Ok, I'll try that.

That was the problem, thanks for all the help.  I'm going to install a new pci parallel card as I have a couple of open slots.
Hopefully, I'll be good to go soon.

I will keep my fingers crossed for you. 

Tweakie.