The processing of control points in volume/surface creation in mri_normalize, used by csurf and recon-all, is broken for certain types of data in the 20040218 release. Please download one of these updates if you are having trouble:
Darwin, 872KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Darwin.tar.gz
Linux, 1263KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Linux.tar.gz
To unpack, move the file you download to your freesurfer/ directory, cd there, and run "tar zxvf <filename>". It will install bin/<OS>/mri_normalize.