Thanks to Greg's suggestions the problem is solved!

I switched from the windows cmtk installation with active perl to cygwin.
For installation I followed the instructions reported in
http://natverse.org/nat/articles/Install...

Running cmtk in cygwin reformatted my 32 bit stacks with this line command:
cmtk reformatx -v --uint --pv -o outputfilename.nrrd --floating floatingimage.nrrd templateimage.nrrd Registration/warp/registrationfolder.list

Francesco