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.