Hans, many thanks for your feedback and your tests. [:)]
The 3D model that causes some problems in the file you posted contains a lot of vertices, and to avoid killing performances, I chose to stop the search of the window surrounding shape if its model have more than 10000 vertices. Maybe I should increase that number if this is the case of many models available on the web, but I would prefer that users describe the shape of the door with the new doorOrWindowCutOutShape property in a SH3F file. I know that the SVG path syntax isn't so easy but it's very handy and short, as shown in these examples.

About the invisible box, please update to the beta 2 version.