afni.nimh.nih.gov

That's correct, 3dTshift does not know the slice order if they aren't transcribed into the header. This is actually pretty common with conversion of DICOMs to NIFTI via dcm2nii or other tools.

You should use the syntax for explicitly setting the slice order, just make sure to use the correct order:

-tshift_opts_ts -tpattern seq-z

Alternatively, you can set the slice order using 3dTcat (-tpattern) or 3drefit. But I usually specify the order by hand in my afni_proc.py commands.