Rob, lots of things make a gun accurate or inaccurate. I think the biggest reason a bolt action is usually more accurate than and auto is the more positive locking of the bolt on a bolt action. The bolt is more likely to be in exactly the same spot with every shot.

I am quite sure somebody out there can write you a book, literally, about the question you just ask.

A note, We have sighted in rifles for 10+ years as a service of our gun shop. I have seen some autos that shot almost perfect, rivaled bolt actions, but over all for what ever REASONS bolt actions in practicallity are more accurate with the least amount of work.