Mike,
I think what you said is make sense, I will check the acceleration between those 3 axis, and try the result.
here is the acceleration setting I had
XY steps per 157.48, Vel 1999.8, Accel 200
Z Steps per 100, Vel 1999.8, Accel 100
Out of interest, what are your acceleration settings. If it losing steps at the end, or start, of a line of code when in exact stop, this could still indicate acceleration problems. You have a huge difference in leads between your X and Y axes and your Z axis. I would expect you to have to have a large difference in your acceleration setting between these also. With a 1" lead on Z, it takes a very large amount of energy to get it moving and it could just be that it is too much.
Mike