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?
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.