There is an updated version of mris_register available for download.
Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar.gz
Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.gz
Download the tarfile and expand it in your FREESURFER_HOME/bin/OS/ directory.