Knocking point may be to low, your spine is probably good. If that does not work (you get poor arrow flight) then your shelf is cut to low for the size of your hand and you need to put a thick leather spacer under your rest and raise your knocking point to match (assuming the bow has a locator or recurve style grip).
When I have my arrow spined correctly, I expect the fletched portion of the arrow to fly over my bow hand. The reason it doesn't do it when you short draw is because the arrow is to stiff and is bouncing of the shelf.