Hi Jeff,
As far as I can tell the Mill is not losing steps, home is a quarter inch ahead of the limit switch, we also use the Z=0 position for tool changing, can change tools all day and not miss a beat, hits the home and stops every time, only time it screws up is when you hit the stop button and the quill makes a hasty retreat.
The other hassle is that if it did it everytime it would be relatively easy to trouble shoot,... it only does it once in maybe 10 to 20 times so it is not a consistant problem just really annoying when it happens. I had read a post from another user that also converted a bridgeport he was having the same issue and he used his limit switch to trip the error line on the servo drive to stop the over travel he said it was the only way he could fix his problem.
Thank you again,
Ted