Hi,
this post would be best on the Mach4 General discussion board, no doubt Tweakie will shift there.
You should not be using Stop (or CycleStop) to stop a job, a hard stop like that decelerates at max and you will lose reference.
The correct procedure is <FeedHold> followed by <Stop>. A <Stop> by itself aborts whatever remaining moves in the motion buffer,
therefore Mach thinks its has made those moves and it at position (x,y,z) when in fact those were aborted and is at position (r,s,t).
A <FeedHold> on the other hand allows the remaining moves, commonly 150ms worth, to execute and drain the motion buffer and
Mach will arrive at (x,y,z) with no loss of reference.
Craig