You say there is no noticeable mis-alignment. I'd say check your alignment like your life depended on it.
I Pop a chalk line on the floor, center the F&R on that, then I use two 8' flourescent lights (for straight edges) zip tied to the rear on each side, as high up as they'll go and still clear the frame/centrestand/pipes. Then measure the gap both sides of the front tire.
It really doesn't take as long as it sounds.