Our Nikon service rep, Steve Fryer, took a look at the confocal yesterday and was able to replicate in a large z-stack the subtle abnormal behavior with the focus motor that has been observed by several users lately. He found that the steps in a z-stack occasionally would get very small for a few steps then "catch up" or come back to normal size. He cleaned and regreased the motor but felt that it may simply be a mechanical problem with no good solution. I'll be contacting the sales department to get a quote on a new focus motor, and at the same time will ask about getting a stage with XY motor control to allow some semblance of stereological sampling capability.
In the meantime, the recommendation is to watch your scans for this phenomenon, save your files as .ids format (for z-stacks), and report to me if and how often you observe problems.
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