afni.nimh.nih.gov

It's expected. It was expected to treat oblique datasets explicitly to oblique/deoblique the datasets. Once the coordinates are aligned, then the warnings can be ignored. The warnings are just warnings, but one day we'll get around to doing something a little more elegant regarding this. In the meantime, see this overview. You may also peruse previous postings regarding obliquity.

[afni.nimh.nih.gov]