This is simplified example with random boxes. In this example we use less boxes, this way we can better examine their locations.
Image obtained in MuPAD. I did here one change - note in MuPAD picture there is an object that is 100% transparent. In JavaView this object was completely invisible. Therefore I changed its transparency to 95% in order to mark its place. The disappearing of the cube was due to fact that in JavaView there is only global transparency for object (no separate transparency for faces and lines).
The same model in JavaView.