Those messages are simply warnings to let you know the NIFTI dataset is oblique, and the standard orientations don't apply. It's likely here the EPI data is oblique and so are the other datasets computed from them, but the anatomical data is not. To handle oblique data in AFNI, consult this web page:

[afni.nimh.nih.gov]

You can oblique the anatomical data to match using those instructions. Make sure your copy of AFNI is up to date also because you should only get that warning message once per program. If you would like to remove qform/sform data, you can do that by first copying the NIFTI dataset to a new file and then use nifti_tool. For AFNI datasets, use 3drefit.