I'm still going to try it, but now I'm skeptical it will work. Anything that fixed it would need to explain why restarting Mach3 fixes the problem, and is the ONLY thing that fixes the problem, plus the acceleration issue.
Any problems in the the spindle, spindle controller, or G540 should be able to be fixed by restarting those, and unaffected by restarting Mach3. That's obviously the opposite of what's happening. That really only leaves the SmoothStepper USB, the SmoothStepper USB plugin for Mach3, and Mach3 itself. Which of course is why I came to post on these forums in the first place.