You should be fine with gfortran 4.9. My current guess is problems with environment variables, since you are renaming directories and not symlinking them, and since you have taken all precautions to ensure that the build directory is clean. Or maybe the Mac build system isn't well maintained.
I see, sadly, that nobody seems to be offering a precompiled OS X binary of NWChem. I wonder how often it's actually compiled/tested on the OS X platform.