The following are some hints to help you identify the problem with the 5 troubleshooting subjects. First, be sure you have your SUBJECTS_DIR set correctly:
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
The trouble with this subject has occurred in the skull stripping step. Check the brainmask.mgz volume carefully, comparing it to the T1.mgz volume (loaded in aux) to make sure that the skull has been completely stripped away, leaving behind the complete cortex and the cerebellum.
The trouble with this subject has occurred during the white matter segmentation step. Check the surfaces to find the spot that does not match the actual boundaries. If you load the wm.mgz volume as the aux volume you will see a hole in this area. If you are looking in tksurfer you will see a hole or dimple in the inflated surface. You can use the "save point" "goto point" commands to find this spot in the volume.
The trouble with this subject has occurred while making the final surfaces. Check the final surfaces (pial and white surfaces) to make sure that they follow the actual boundaries and do not include anything that should not be included.
The trouble with this subject has occured during the intensity normalization. Check the white surface and be sure it is including all of the white matter as it should. If you find an area that is not included as white matter be sure to check to see that the intensity is at (or very close to) 110.
The trouble with this subject is a little tricky to figure out. The midline cutting planes are not actually on the midline, but the real root of this problem is in one of the very initial steps of recon-all. The talairach transform is bad and will need to be fixed.