When the engine boots up it detects the quality of video card available. It categorizes them as Bad, Weak, Slow, Good, or T&L. The engine then defaults to A5 mode for everything less than T&L quality "like GeForce or Radeon." I forced A5 mode on my Quadro just to make sure that was indeed the problem.

I don't have their transparent set to on or anything--I'm using the shader exactly as it was posted. But they do look like they're transparent. What do your objects do when you force A5 mode?