I re-ran over 400 scans by using Freesurfer 4.3.0 on Mac OS 10.5.6. Well, I’m very happy on the results. Anyway there are two issues I encountered:
1) I have 3 scans hanging on the last second step when creating the aparc+aseg.mgz by using mri_aparc2aseg (more precisely  is  the “labeling slice” processing)  for over one week though it finally finished. The log is attached.
2) I have some scans reported “mris_fix_topology failed! (euler number != 2)” so recon-all exited with errors. I didn’t find there was any problem when I used the V4.0.5. I attached the log as “recon-all2.log”.

Thanks.

Wayne