I'm a bare shaft tuner. You need to shoot bare and fletched at the same time. Try shooting three or four fletched shafts and two or three bare shafts into the same group. Shooting bare shafts alone without fletched to compare to all you can do is watch the arrow in flight or how sticks in the target...there really is no reference. Sounds like you were really close though if just a bump of the nock point cleared things up. Bare shaft tuning is touchy, one reason it works so well...
I have read in the past, and it sounds reasonable, that a slightly nock high tune is more forgiving than the "perfect" straight and level that we all try for. The theory is, if I recall correctly, that if you tune so a bare shaft is flying perfectly straight and level on a perfect shot, any non-perfect shots might send the arrow from the bow either nock high or nock low. A bow tuned to shoot slightly nock high from a perfect release will still shoot nock high even with a non-perfect shot. There is still an error and deviation from perfect flight, but the deviation is all in the same direction, i.e., always nock high.
I still like to see my bare shafts in the center of the fletched. In the end what you want is broadheads and field points hitting the same spot with good arrow flight. If you are there, don't sweat what you did to get there.