The view and space of the dataset are not being interpreted in the way you expect. This command will show what view the AFNI GUI and other commands will assume from the header of the dataset:
3dinfo -av_space mydset.nii.gz
In some cases, the header of the dataset shows an ambiguous code that can either be in a standard template space or in a native space. You can set AFNI_NIFTI_VIEW to be either orig or tlrc.
You can enforce a particular space, like MNI, on a dataset with
3drefit -space MNI mydset.nii.gz
