Dan,

I uploaded an updated version of the CMTK Cygwin binaries: https://www.nitrc.org/frs/download.php/9901/CMTK-3.3.1-CYGWIN-x86_64.tar.gz

This is build with the latest Cygwin x86_64 libraries as of today, so if you have any library version mismatches, those should disappear after updating your Cygwin install (sounds like you already did) and installing the package above.

Best,
  Torsten