Did you try to export extruded building footprints from ArcScene as multipatches by using tool "Layer 3D to Feature class"?
There is a known issue with Background geoprocessing.
NIM102064: Exporting extruded polygons to multipatch with the 'Layer 3D to Feature Class' geoprocessing tool does not preserve extrusion if 64-bit background geoprocessing is enabled.
You could disable the Background geoprocessing under menu Geoprocessing > geoprocessing Options > uncheck the "Enable" check box for Background Geoprocessing.