Make sure the UV shell edges are hardened on both. I use this script all the time: http://jonathonstewart.blogspot.co.uk/2012/10/script-harden-edges-of-all-uv-borders.html Apply that script to both meshes, then rebake and see how it turns out :)
I get what you guys are saying but I'm not fully sure I understand what I need to do. I usually bake down onto a fully smoothed low poly, i.e. a model will all faces set to one smoothing group. Are you saying that in order to fix this all I really need to do is define my smoothing groups better leaving hard edges hard, and…