Bob Popovics did a bunch of research on that a few years back when he was working on his Jiggy fly. The theory is that the material causes drag in the water and whatever side of the hook the majority of the material is tied on is the side that will be the top when it's being fished. So if you tie an upside down Clouser(hook point down) it will fish with the hook point down regardless as to what side the eyes are tied on.