Try to post an example of the exact command you used. To copy a NIFTI file to AFNI format for any particular view (orig,acpc or tlrc), you can always do something like:
3dcopy dsetorig.nii dset+orig
3dcopy dsetacpc.nii dset+acpc
3dcopy dsettlrc.nii dset+tlrc
If you want to change the view of an AFNI dataset, you can use 3drefit
3drefit -view tlrc dset+orig