Some more info:
The affine matrices in the (input) niftis all are the same.
These are relatively narrow-angle scans (back of the head).
So I guess that makes the alignment harder.
Here are means of the raw (pre-fmriprep) images:
Here they are after:
To my eye 3 of those are perfect, two are poor and one (the top left) is very bad. How do I track down the problem?