Hi Richard,
Sorry to hear about all of the trouble you've been having. It is strange how USB works flawlessly for some and not for others. Thanks Hood for your determination in getting to the bottom of this one.
I would guess that you would have the best luck shortening the USB cable as short as you can (6 inches if possible), and then using parallel port cables to go from the SS to the breakout boards. I can't guarantee it, but I have had users fix USB communications problems that way. Another possibility is to run a heavy duty ground wire between the SmoothStepper and the computer, in parallel with the USB cable. I suspect you might have a ground loop present, and while it would be best to eliminate the ground loop, you can minimize it by minimizing the impedance between the computer and the SS. Another trick that can help is to insert a self-powered hub in between the computer and the SS. A hub can help regenerate the USB signals and interfere with the ground loop. It would be interesting to see if you can measure any voltage difference between the ground of the SS and the ground of the PC. You can also try plugging things into different outlets. Please let me know if any of this helps. If it doesn't we'll keep at it.
Thanks,
Greg