This is very odd.
I've got a scene which has final gather and GI turned on, and uses a textured object (I refer to this as my "light dome") with an HDR image on it as the main light source. The visibilty of this object is turned off in the mental ray flags so that it will light the scene, but not render. This works great for everything except objects with transparencies on them. What happens is that where the object should be transparent, the light dome renders. Also, the alpha channel no longer seems to recognize the transparency and fills in the whole object.