I cannot say what the problem is. However, I have successfully compiled NWChem 6.1 on cygwin using the following:
setenv NWCHEM_TOP <your path>/nwchem
setenv NWCHEM_TARGET CYGWIN
setenv NWCHEM_MODULES all
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran >& make.log