Even if it messed up a few projectiles after the one that was upside down, does it really matter if it messes up a few afterwards? If you were to put a bit more of a bevel on the hole that feeds to the die so it lines up? i thought all it would do is to flatten the nose from the punch.
Jmorris - your design looks pretty simple, a hole saw and a piece of round nylon. I'd just make one for each projectile shape and have a mark so i know where it must line up every time i change it.