Anderson-

Just remember that DICOM and NIFTI use a different coordinate systems
   https://www.slicer.org/wiki/Coordinate_systems
I am not familiar with NiBabel, but I suspect this explains the difference.

To convince yourself of this, look at a scan in a nice DICOM aware tool (like Osirix) and then the dcm2niix converted DICOM with SPM. You should see that the spatial position is preserved, it is simply transformed to a different coordinate system. We do this with the NIfTI SForm and QForm so that the raw data is losslessly copied unchanged. By the way, I usually like to place a vitamin E capsule on the left temple as a fiducial marker. It shows up nicely on the high resolution T1 scan (where segmentation has no difficulty segmenting it), but is invisible on the DTI/fMRI sequences so it has not impact on motion correction.