Check that you are configured to see the patient view rather than the image-referenced view, which you can set as described in the link below. Note you can also volume render or make the slice views visible in 3D to see the effect of the transforms.
As a side note, nii files are slightly lossy because they store the transform with 32bit floats while Slicer internally uses 64bit which is better preserved in formats like nrrd and dicom. This may sound like a small detail but it can lead to visibly different results or numerical errors when comparing orientations.