Just to be clear: Your data for the building heights, is that height above sea level, or height off the ground at said location? Since your units seems to be good--according to what you have said. Let us know. Just to reiterate, I once had to delete the DEM heights from the building heights to get a true height for a project I worked on. Just making sure it is not something simple like this. Good luck.
What is the coordinate system units of your data and CityEngine scene? Are you pulling this value from the attributes? What units should it be?
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