Sorry, I should I have made it more clear in the example what I am getting at. What I tried to point out here is that the Z position jumps from 9.94550 to 9.99550 between the first and second point contrary to what was programmed.
The stage is definitely moving, including a backlash, between the individual points. This specific example has indeed a very small step size but I had it happen at much larger steps as well (but I would have to do some digging to find good examples while I had this one at hand).
In the past, when I caught it in time and the sample was still in the machine and check, I could also see every time that the first point of the transect was focused and all subsequent points were defocused.
I'll see if I can find more examples at varying step sizes of this behavior.
Anette