"C:\cygwin\home\username\cmtk-newbuild\bin\reformatx -o C:\Users\username\Desktop\fileout.nrrd --floating C:\Users\username\Desktop\filein.nrrd C:\Users\username\Desktop\reference.nrrd C:\Users\username\Desktop\warp.xform"

It does the transformation (it takes time and I get warnings as I usually do about valid orientation info) and then the path to save is wrong, but as you see form above it is the same path as I am reading from.