Nothing is changed. I'm starting with a simple building polygon and extruding it. I'm using the GP tool, 3D Analyst Tools/Conversion/Layer 3D to Feature Class. My units are all the same and I've tried using a) only the feature in ArcScene by itself and b) with a DEM source and baseheight/extrusion based on that. In both cases the results are: a) a flat multi patch, b) the wedge as shown in the image.
CityEngine is not an option since I don't have a license for that.
I'm using 10.1 SP1, Win7 64B OS.