I had just the opposite problem: for some of my subjects the 3dSkullStrip cuts too much around the pre- and post-central gyrus. And after I warp the EPI to the template (I was using the MNI template shipped with FSL since that one is less blurred than the version shipped with AFNI), that part turns to protrude outside the brain. However I found that by now freesurfer gives me the best skull-stripped brain (better than I can get from both AFNI's skullstrip, skullstrip after uniformization, and some FSL bet command my colleague suggested me to try)
And the warped result is also better based on the freesurfer stripped brain.

I am curious if there is any thumb of rule what parameters would be best for templates of different resolutions (from the sharp N27 to the somewhat blurred MNI template from FSL to the more blurred version shipped with AFNI).

Thanks!