I think the Skull has to be a child of the right hand. Magnets I think I like normal independent layers (has to be under the parent mesh to attach to), but you can turn them off. It looks like the SKull is a separate puppet?
Hiding things making other things change I have seen sometimes due to swap sets. I would double check he swapsets have the layers you expect in them. Hiding one reveals others etc due to swap set membership. That is my best guess.