Could the SS perhaps have some additional HW noise filtering that would help? Probably yes. Would it solve all these problems we here about? No.
The first lines of defense when building a machine are proper (earth)grounding and proper isolation (optical or otherwise). Most machine control I/O boards will NOT have optical isolation built in as some of the external boards that are driven (like Geckos) also have optical isolation on their inputs. It is best not to 'stack' them. For example, I refitted an old Bridgeport with a Galil motion control card, the card, the extended I/O board and the breakout board from Galil cost about $2500 and they were not optically isolated. They did offer an isolated version of the breakout board though. I used solid state relays instead, as two Opto22 boards fit in the same place as the old main I/O board did. The solid state relays not only gave me the optical isolation, they also allowed me to switch different voltages directly, both AC and DC.
The problem comes about when folks, who don't know any better, build a machine and don't quite get the wiring neat and tidy and also don't get the grounding done properly. Through in the lack of any form of isolation on most if not all of the I/O and you have a problem. You thorw a SS into the mix (or any USB device) and the USB cable will pick up all that electrical noise causing the main hub in the PC to stop trying to communicate as it says, heck there is a lot of noise here, I can't even hear myself think!". The problem in the noise.
Don't take that the wrong way. I'm not picking on the OP or anyone else. We all start out at the same place, and learn as we go. But, we need to learn what the source of the problem is and improve out own machine building practices too.