Hi,
Sometime back i had the same problem and tried several options including other software like geomagic and cloudcompare. I got the best results for my problem with CMF ROI registration. I validated the results of superimposition with Model to Model distance and shape population viewer.
I think if you go through the following link you will find useful inputs from many here.
We have done similar things with 3D Slicer and i do not think it is related to the thickness of the cortical bone.
Also why are you segmenting and registering at the first place ? Is it not best to simply do Image registration ?