You nock the arrow over the nock point? As I understand it, the reason for nocking under the nock point is to keep the arrow from kicking off the string upon release. I think your nock point may be too low, and you're banging off the shelf. Raise it up, way up, and slowly lower it, shooting bare shafts at each new set. As soon as you get rid of the nock-high, stop there.
Don't give up on bareshafting. If you can get an arrow to fly pretty well without feathers, it won't be fighting the feathers and losing speed and power as a result of them pulling it into a straight line. (If your brakes on your car are pulling to one side, sure, you can put opposing pressure on the steering wheel to keep the car going straight, but you end up sacrificing forward efficiency.)
EDIT: I just saw that last post above mine. I'm not trying to argue here; my bareshafting isn't perfect, because my form isn't perfect either. But the better a bare shaft flies, albeit shot with imperfect form, the fewer uncontrolled variables you have. The feathers should be the last resort element of arrow flight, not the catch-all, end-all to make up for poor tuning.