Hi Ben,
Are you using the 3D Layer to Feature Class tool in ArcMap or ArcScene? The tool uses the 3D layer properties and creates the multipatch. In ArcMap there are no 3D properties, so the resulting multipatch would be flat. You will need to run the tool in ArcScene with the 3D properties applied to the layer.
How Layer 3D To Feature Class (3D Analyst) works
-Timothy