Hello Dana,

I'm afraid that the Windows installation has generally been unreliable. Right now the best thing that I can suggest is

1. Install the CMTK software directly from nitrc (I recommend the cygwin versions rather than the pure windows versions)

You can see some tips here http://natverse.org/nat/articles/Installation.html#cmtknat-on-windows

2. Use the Fiji CMTK GUI to generate shell scripts 

3. You can than edit the scripts to replace the location of the munger script and CMTK binaries

"/Applications/Fiji.app/bin/cmtk/munger"

"/Applications/Fiji.app/bin/cmtk"

with their installed locations

in the terminal to find them.

Best,

Greg.