I just ran a print that was 4mm, and DWC showed 4.1. The layer height was .2mm, so there should have been 20 layers. It printed 21. When I remove the zhop from Slic3r, the file shows as 4mm.
I posted another thread here where I felt like my first layer is being smashed down. It apparently is because it is printing the first layer at .1mm and the rest at .2mm.
I would rely on firmware retraction, but the zhop is a bit too slow compared to Slic3r. I posted on the Prusa Slic3r forum, and the conclusion was that because the preview was showing the correct height it was not a Slic3r issue.
What could be causing this?