The NIfTI SForm is a 3D Transformation Matrix, which encodes the distance between voxel centers, the rotations and the distance from the origin (raw data: MRI isocenter or normalized data: anterior commissure). For your data, the 3x3 rotation matrix will only appear as [2 0 0; 0 2 0; 0 0 2] if you acquired the volume orthogonal to the bore of the scanner. However, in your case the slice orientation was angulated with respect to the scanner's axis. Your other scans were acquired orthogonal to the scanner bore.