Sort of misunderstanding. Normally you do the Smooth test once till you found your LRS setting. But in the beginning when you do not know LRS and URS, you might get misalignments because both settings might be a little bit out of NPP. When I found my LRS for my camera and change the lens I try to find my URS and of course do not touch my LRS. Plus you do not have to check LRS with different pitches because you have to shoot 2 rows for example. Pitching up and down with the horizontal arm will keep the NPP because you move in NPP.
Could you please send the solo pics of your URS with http://ge.tt/ so I can check them in PS? I feel the reference is still moving a tiny little bit. You see a sort Knob in the top of the white line on the left side, which you can not see in the centered shot.