I don't know the mechanics of why, but I do know it is not always a given a bow will tune with an arrow exactly level with the rest. I have had plenty bows tune nock high and level, but never low. Different arrows, draw weights and lengths, variations in limbs, along with various grip positions, make archery tuning difficult at times.
I don't think anyone wants to be nock high, but if that's how it tunes, then let it be.
I'm sure someone else with more technical knowledge will chime in to explain.