Ok, I think I implemented the changes you mentioned, reran both cake and make and it worked ok.  
I am having some problems though running some cmtk commands.  For example, when running the 
reformatx command I get an error when attempting to write the nrrd image:
"ERROR: NrrdIO library returned error '[nrrd] nrrdSave: couldn't open("cygdrive/c/cmtk/cmtk_newbuild /bin/\Users ..."

I think this has to do with what the home directory and where I am running the commands right?  Even if I run a command from a dos terminal it gives me this error.  
Any thoughts?