I have installed CMTK 3.3 on windows as well, and I am experiencing the same error when I try to use warp.exe. It said the file does not exist. I am trying to run .nii files.

Reformatx also gives an error: 
The file/directory C:/registration/working/warp_output_transform does not exist or cannot be read

I will try install the Cygwin version.