If you are finding this with NIFTI datasets, then you may need to reset the sform or qform codes for the dataset. For AFNI datasets, those will only appear if your datasets have the +tlrc view. You can reset the datasets (AFNI or NIFTI) with
3drefit -view tlrc mydset+orig
If the NIFTI datasets are often misformed, then you can change the AFNI_NIFTI_VIEW to tlrc.