Hi Kate,
afni_resproc.py is pretty dated--I wrote it about 3 1/2 years ago when afni_proc.py didn't support all of the resting state options that it does now. Since then, all of the missing functionality has been added to afni_proc.py, while afni_restproc.py hasn't been updated in three years (and won't be in the future). So, you may want to refer to afni_proc.py's examples 9 through 11 and go from there.
To answer your question though, afni_restproc.py doesn't ever call 3dSkullStrip directly, so the problem you're seeing is probably either in the call to @auto_tlrc or align_epi_anat.py. My guess is the latter, but I can't say for sure. You may be able to fix the problem by using the -script option and then editing the offending call. For example, adding "-epi_strip 3dAutomask" to the call to align_epi_anat.py *might* do the trick.
Rick,
I think it would be worth adding a note to afni_restproc.py so it's obvious that it probably isn't the way to go for people who aren't already using it. Something like "WARNING: afni_restproc.py is OLD and (largely) unsupported. For the latest and greatest, see afni_proc.py" at the top and bottom of the help output seems appropriate.
Rayus
