Thanks for pointing out that thread Neale -

I found something funny happening to the Y axis in my UCCNC software, where my slaved axis was re-copying settings from another axis, including the wrong step and Dir information when I changed a specific value on one of the pages ( I'm not talking about the value of boxing slave, it's something else like if I make a change to the acceleration value, then the slave dumps all info and re-imports all info including the wrong pin and direction assignment ) . I still haven't figured out which value it is because I don't change the settings enough, but the randomly see my Y axis trying to go opposite directions as a result sometimes of me changing a few parameters.

When I went back in to fix the issue ( not knowing why it had changed, or how ) in the confusion of trying to get my Y axis motors to spin in the right direction ( together ) - I Clicked on active low, so I had some dir / pin steps on active low, and some on active High for my X and for my Z axis.

Guess where the errors were in my cut - in my z axis was the biggest, but X also had a left / right 1-2mm error by the end. So hopefully in a couple hours I can restart the beast up, and get my first workpiece cut out !