There is an anomaly in the plugin which gives a small error in position but it does not accumulate so it will only ever be that value out. Greg has sorted this in a test plugin but unfortunately it has introduced another small issue but Greg knows how to sort it, problem is it requires a rewrite from the ground up so its taking some time.
I wouldnt worry too much about it for the time being as it is just about 0.001mm which I dont think will affect you
Out of interest what are your steps per unit?
Changing motor settings will require a restart as the info gets flashed to the SS each time Mach starts.