I have only now gotten around to testing the problem that I submitted in the beta but the problem is still there in the 4.0.2 version. What happens is that brushes (or parts of brushes) become transparent, as you can see in the image below.
I’ve just selected one brush here but it’s doing something strange (with the bsp cuts?). If I go into wireframe and select an “invisible” brush, then go back to lit, the transparent part gets another texture (image 2) and the light breaks.
https://dl.dropboxusercontent.com/u/8909833/Images/bsperror.png
https://dl.dropboxusercontent.com/u/8909833/Images/bsperror2.png