We fought this issue for about 2 weeks , just a few months ago.
I replaced USB cable, changed computers , added groundwires to everything ....and I mean everything ! I was just about to order a new com . board when I told the guys in the shop to go ahead and PM the machine while it was down.(Clean everything, replace and recut spoil board, regrease gears etc)
Long story short, the communication issue went away !
We started having the same Comm issue a few weeks ago, and found that the roller alignment was off on our carriage. We realigned the carriage and haven't had it since .
Conclusion:
It may sound silly, but it seems that the gears being dry, and the carriage rollers may have been causing an excess of electrical noise and causing the loss of communication.
Our other machine also had the comm issue when we had the USB bundled and zip tied with all the other cables. We seperated it and went with a double sheilded cable and haven't had the problem since ......KNOCK ON WOOD !
For starters though , ground everything to everything and make sure all grounds are properly connected to the ground lug in the control. I saw a grounding diagram somewhere. It may be on the SB sight.