Thanks for the reply's. In true fashion, I finally gave in and asked then went back to it and tried more things. I changed the step setting to 1/8 from 1/16 and slowed it down considerably (although the old speed setting worked with the original controller) and got it working. I will try changing the pulse widths too as I'm still not 100% with it right now, although it is getting things cut for now.
More settings testing to follow....