Then it's not some odd stuff on your hardware. What happens, is that you don't see the face as it doesn't exist. During the VIS process however, it was treated just like any other world brush/face. So faces behind it aren't rendered, whether you applied the null texture to it, or any other texture.
A good trick to prevent this is to check with gl_wireframe 2 on. Can you see wires behind the whole face, from every direction? Then you won't get a HOM effect when you cover that face with the null texture.
Ah, well, you understand by now, I guess...