I've noticed one thing about ghost bones, and maybe it was just me, but if I don't group the mesh going in to the setup room and apply the donor rig with the ghost bones and auto group the mesh when I apply the rig, they are not ghost bones on the new mesh. If you take them out, you get the polys not grouped to a bone error when you exit the setup room.

If I had a nickle for ever time a woman told me to get lost, I could buy Manhattan.