I have spmregister (and spmregister-sess) working on 64 bit machines. The fix is to set the FS_SPMREG_MATLAB to point to the 7.0.1 version of matlab. In the NMR Center, you can just:
setenv FS_SPMREG_MATLAB /usr/pubsw/common/matlab/7.0.1/bin/matlab
You can do this without affecting the version of matlab that you normally use. This will also work on 32 bit machines.
doug
freesurfer@nmr.mgh.harvard.edu