I totally have this problem... but only from time to time. The best way to coax the machine to spaz out in this fashion is to stick down two panels on the machine... Zero it to the first panel and run the program. THEN, I go ahead and jog over and zero it to the next panel. Upon pressing "START" the machine jerks, as if just a pile of pulses get sent out to one or more of the axes, then, even though the DROs are reading right, the machine screams over to the first panel, or at least somewhat, and starts mutilating it. Usually, since I have a slow to spin up spindle, I can catch it before any major damage happens, but I'm always on my toes. The smoothstepper is great and all, but I use my machine to make money, and when I maul a $200 sheet of plyboo because my controller goes haywire...well it just makes my day a whole lot less fun. The real sucky part is that I can't reproduce this problem in any reliable way, but I'm taking notes on when it happens, and it almost always happens after a run and a re-zero, and not when I press start, but when I press start the second time (after the tool change notice) Also, I've never run this machien with any other config files. it's been smoothstepper since day 1.
Anyway, my feedback. I know this thread is old, but I'm kind of at the end of my rope with this.