There's a new version of mri_watershed available. The fix is to eliminate s problem with the WM value. The previous version sometimes used the pon area for the WM value.
Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.gz
Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar.gz