I’ll give it a try and get back to you.
It almost looks as though the atlas is being registered to the original anat_t1.nii.
Are the anatomy slices in the 3d viewer taken from the normalized preop images (glanat.nii)? I have Preop MRI selected in the drop down of the Anatomy Slice controller. Is it possible that the atlas is being resliced into the original anat_t1 space?