Man, I have been pulling my hair out over this. I went out and bought a video card, parallel card, and new motherboard and figured I would start with the cheapest and work my way up. I first tried the video card - it didn't fix it. I then tried the parallel card and that didn't fix it. Lastly, I installed the motherboard and completely reinstalled Windows. While Drivertest was pretty happy about all of this (practically a completely flat line), it still didn't fix it. I even had an old computer that was similar to the one on my working machine so I dug it out and tried to use it and even it would not work.
OK, so I took the config file from the new PC and plopped it onto my working machine (backed up its config first) and guess what - I get the same behavior on the working machine with that config file. Previously, I just went in and modified the ports and pins when I connected it to the new mill. I took the original config from the working machine, put it on my new machine, changed the ports and pins and it works!
So now I have boiled the issue down to a difference in the configs and I really want to know what it is. Had I not had a working machine, I would have probably just cranked this one down super slow and figured thats how it should be working.
I downloaded the XML reader and went through it but the new (non-working) XML is twice the size of the working one. I also don't know what every setting means. I have attached both XMLs if anyone would be so kind as to help me identify it.
Editd to add - I did notice that Sherline mode was on in the working but that isn't the cause. I tried that setting on the non-working file as well.