I think the most likely explanation is conflicting information between the NIFTI header and the AFNI extension in one or both of these files. You can check the voxel sizes AFNI uses with 3dinfo on each dataset:
3dinfo -prefix -d3 *.nii.gz
If these are different among these and different than you expect, then you can remove the AFNI extension from the NIFTI header with this command:
nifti_tool -rm_ext ALL -prefix dset1 -infiles dset.nii.gz
Take a look at this previous thread to see how to work around this confusion:
[
afni.nimh.nih.gov]