Creek, Nock left and right causes more confusion than any thing when tuning. Few if any of us can shoot consistant enough to shoot a bare shaft without some left or right kick. The trick is to seperate what is tuning caused from what is form caused.
First, set your bow up EXACTLY the way you are going to shoot it, as any changes you make after the fact changes the tuning. Including tip protectors, bow quivers, string silencers, ect.... Next set your brace height where you get the least noise and vibration. Don't set it inside the bowyers range and call it good....Set it low, shoot 4 or 5 shots, twist up the string 4 or 5 twists, shoot it again...Keep doing that until you find that "sweet spot". Measure it and record it so you can duplicate it as the string stretches and or you change the string.
Tight nocks can cause a bunch of problems and I'll bet is part of yours. Your arrow nocks should fit only tight enough to keep the arrow on the string when pointed down, lightly tap the string and it should fall off. Any tighter causes problems.
At this point, you are ready to start tuning. Take 3 or 4 fletched shafts and 3 or 4 identical bare shafts. Get back at 10 yards or so, and start shooting all the arrows at a spot. DO NOT PAY ANY ATTENTION TO NOCK DIRECTION. What you are looking for is where the arrows group. If the bare shafts group below your fletched shafts, your nock point is too high and vice versa. If you lower yopur nock point a lot and they still shoot low, that means your nock point was too low to start with and is kicking the tail of the arrow off the shelf. Styart way high (1"

and bring it down slow.
If your bare shafts are grouping left of the fletched shafts, your arrows are too stiff, increase point weight, or use a thinner side plate. If they are grouping right, your shafts are weak, decrease point weight, shorten your arrows, or increase side plate thickness. Once the bare shafts and fletched ones start grouping together, you are getting close. Back up to 20 yards...Start over.. In a well tuned set up(and if you are good enough), you can group bare shafts and fletched shafts together out to 40 yards or more.
Some things that cause confusion....Changing more than one thing at a time. If you do that, and things get better or worse, what caused it? You don't know, only change one thing at a time. Going from a 2020 shaft to a 2117 is not one change, it's two, you changed arrow spine and centershot because the arrows are different diameter. If you make a single change and things get worse, put it back and go the other way.
Shoot lots of arrows and go by the "average" between them. A bad release or other form problem can cause a stray, ignore it, never base changes on just shooting one or two arrows. By shooting lots of arrows and looking at the average, you are seeing the tuning problems, not your form problems.
Good luck and hope that helps. If you want even more details, go to this link and go to the "tuning" page:
http://www.bowmaker.net Good luck...O.L.