Can you run one of the individual registrations to get more info about the error. e.g.

cd C:\CMTK_Registration\CMTKreg

C:\CMTK_Registration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\Ref20131120pt14pl2_MIP318zf01_9dof.list template/Ref20131120pt14pl2_Randlett_stackrev_01.nrrd images/MIP318zf01.nrrd