What is strange about the G0 problem is that there are only two reports of it. I've sold 50+ SS and have not had a customer have that problem. I suspect there has to be some obscure Mach variable being set in the profile, perhaps one not even visible to the user, that causes this. A similar now defunct mach Variable is responsible for a Limits responding slow on the SS, Greg found that problem and is taking care of it now.
Lots of teeny-tiny moves will make things creep as the machine is trying to accel/decel on every one of them. You might try turning on CV mode and see if that helps. When you combine a huge file and a high pulse rate you are creating a big strain on the CPU so the precise timing needed by the parallel port driver is not possible.