New clone DNA i'd say along with recruits. And if you notice in ANH there are a bunch of Stormtroopers in varying heights so I get the impression they were having a pretty good recruitment rate at that point. The ones that ran away from Han must've been noob recruits. But the Rebellion's victory must've brought down recruitment rates to an all time low. In ESB and ROTJ the troops are all the same height. Maybe they had to go back to nearly all clones.

Or the Emperor was paranoid of spies after the victory (not that a lowly trooper would have much access to information).