Another couple of ideas -

Try the "describe" tool like so:

describe.exe Ref.nrrd

That should rule out any issues related to the more complex sequence of command line arguments for "registration".

And see if a different image format works. For example, try a NIfTI file (.nii, or .hdr/img pair).

There is certainly a possibility that the Nrrd reader specifically is having problems.

Best,
  Torsten