Not trying to speak for Neil here. I interpreted it as are you certain your Z axis moves the exact distance you tell it to. For example, when you command the Z axis to move 1 inch, does it actually move one inch.
Calibrate your Z axis to make sure it is traveling the distance it should. Actually, you should calibrate both the X axis and the Y axis too. There are are few good threads in the forum that will describe the process. Search for calibration.
I used a standard ruler to calibrate my Z axis. My understanding of the process is, the longer the distance you use to calibrate the more precise you can get. All Axes are limited to their respective travel length; the Z axis being the shortest.