Hmmm......maybe time to look at what your steps per and velocity are in motor tuning and check the SS setup to be sure you're setup fast enough and not too fast.
Read thru Jeff Birt's SS setup doc here
http://www.soigeneris.com/Document/Installing_and_Configuring_the_SmoothStepper.pdf Read the last couple paragraphs on Page 9 and get your head around this. Check your motor tuning numbers, do the math, and be sure the SS setup matches. I'm not sure if something here can cause what you're seeing, but seeing as you're new to the SS, Jeff's setup doc is a must read anyway. It's impossible to know TOO MUCH about this stuff!!
Also, you stated you "started over" with a fresh XML. How did you do it? Clone the Mach3mill profile and re-enter all your setup info? That's the ONLY certain way to be starting fresh I know of. This exercise will give you cause to document your entire setup, too!!
An aside. I don't know how to do it, but someone who does should write a script or something to extract all the Mach3 settings, Ports & Pins, Motor Tuning, Homing & Limits, etc., to a text file or something. I do it with a combination of screen shots and Excel spreadsheet, but it's a pita amd every time you change something you have to remember to update your stuff.