I think you may be having problems with the USB SS losing communication for some reason. It could be related to the problems others saw due to noise, in fact I saw this on one machine and the cure for it was to remove a couple of components on the SmoothStepper to isolate the Gnd connection of the SS from the Computer. I think you can do the same by cutting through the shield of the USB cable at the SS end of it.
I will see if I can find the thread regarding this issue and paste in a link in a minute.
Hood