Hrm.  My issue is the reverse; g-buffers appear to work normally, but turning on Alpha Channel messes up the render.  I watched it render a couple of times; the render was normal until almost done, then the alpha channel washes over it, destroying it.

Just did another render with alpha channel off, one g-buffer in.  G-buffer shows up normally in PhotoShop (object index) and appears correct.

HOWEVER, I can not be entirely certain the g-buffer isn't being added to the image.  I suspect it is not, as I am using a plane with a transmap on it, and I would think the original shape as displayed in the object index would give itself away....