You went a little further than I did.  I had the exact same problem, and my solution was to wrap my USB cable around/through a ferrite bead.  I also wrapped the DC wires going to my VFD's around/through a second ferrite bead.  One other thing I did was I added a 10uF cap to the +5VDC and 0VDC terminal on the SS board.

Hope this helps some too.

I have had the same issue. I have  USB SS  and  5 meter USB cable. Additionally I have 2 spindles with 2 VFD  running same time. Without  any preventive action I could run 4 or 5 minutes then  mach3  was freezing .  After reading your recommendations  I put  2 ferrites  to both ends of USB cable. It helped. Frequency of random stops is decreased  but didn't solve completely. Then I have ground my machine. I t didn't help at all.  I have put another wire shorting to machine chasis  and shell of USB input cable of SS.  There is no freezing at all now. I can run at 4 khz setting. ( due to my pc can't meet demands I have dropped it to 1 khz later)  At beginning  I can't go over 500 mhz.  I hope this will help the people facing same problem.

I have a USB Smooth Stepper on a Foam cutter. I had the same issue were it would loose comms. at random, but mostly when the hot wire turned on which i a pretty big surge.
Two things to try:
1) First power the SS from a 5v supply within the machine. There is a jumper on the SS that you need to move to separate the Computer 5V from the SS.
2) If #1) doens't work use an USB isolator. That's what finally did it for me.