If it helps any I was/am in the same boat. Either check Sherline mode or lose steps in Z. I haven't changed the pulse width though. G540, 48V power supply, keling 387's all around.
It's not so much that it happens like this, but that there seems to be no logical explanation for why. Gecko says there is no reason for it to be this way, and it doesn't make sense why it would be. I've recently upgraded my computer, but I'm still using the old XML. Perhaps the computer upgrade will have helped some as the old system was a bit on the low side of spec.