Wow I have no clue what you did to cause this but it looks really interesting.
I think you do need to unwarp absolutely everything on the mesh you are baking to. It would be very unwise to not do so because then the UV islands may be un-proportional. What I means by this is that you never want select some UV islands and scale them to a different size than others because that would make the resolution look higher or smaller on the part.
I have never seen anyone unwrap just part of a mesh and baked and maybe this is the reason. I would unwrap everything, then bake again with clear on to clear the image.