afni.nimh.nih.gov

It is difficult to say without being able to investigate.
But since you can run 3dSkullStrip directly, the current
shell setup is good, while trying it in a new shell (via
one of those scripts) fails.

Go ahead and edit @auto_tlrc to echo that
DYLD_FALLBACK_LIBRARY_PATH variable. It will
likely not be set. On a related note, what is the output
from:

afni_system_check.py -check_all

- rick