Is the cup screwing in enough to touching the frame's edge? Or is that the problem when you say sticking out? If that's the problem you might need the frame threaded in further so the cup can screw in far enough to touch the frame?
Maybe you are using a spacer that is pushing the cup too far out and causing the crank's spindle to not have enough spline to tighten to? Im just taking a stab in the dark here. Pictures maybe, or a picture online that represents the problem?