Hi Don,
Seeing the same problem after switching over to a servo system is weird indeed! But then, as Roger noted, I am curious if you were merely bench testing with the servo or it was really driving the machine. But my curiosity has other reasons, and I am afraid I have to disagree with Roger. While an unloaded servo will act absolutely differently and will need careful tuning, there is absolutely no reason for it to move to other locations from those commanded by its driver.
I am very doubtful it's a software bug thought, since you have abstracted it to merely:
PC -> Mach3 -> Parallel Port -> Gecko(/Viper) -> Stepper(/servo)
Thousands of people are using exactly the same setup and no one has reported this. So either they don't have this problem or they just never discovered it. I think its the first option.
After you eliminated a possible wring issue, and considering the above said, the only two links in the above sequence that can be the problem are PC and Parallel Port card. You have switched between two absolutely different PCs with no change. Can you try setting the PP to different mode? This usually has no effect, but who knows... I remember Brian or Art once had a recommendation for the particular setting, but can't seem to recall what it was, so you'd have to try them all and see if it makes any difference. I know your findings show that a break out board looks to be having no effect on the problem, but I wouldn't recommend putting it back into the above sequence - not until you find the most abstracted sequence that works and then start adding things to it and see when the problem appears back again. This is again, just to eliminate any possibility of a combination of things.
So see if you can play with the above sequence, trying out every possible combination of PC and PP (card and settings). Another way would be if you could put your hands on some external motion controller, like the Smooth Stepper.
Dan