Looks like the round base is aligning okay but the ears are way off, there must be some major deformations in the scans themselves. Can you show us a screenshot of your calibration? Are you filling the camera with as many points as possible? I assume this is SLS? More info on your setup might reveal a clue. I would try doing a global fine registration several times, you might see the meshes move quite a bit. Keep doing it till you can't see any more movement. If nothing improves you might get slightly better alignment in the body if you cut away the base and do the body separately.
DealExtreme red line laser, Microsoft Lifecam HD-5000