I thought it was implied that he had something going on before the time skip too, because he got tired easily. Or maybe that was just the strain of his eyes
It was never said. Hell we could use his fight in part 1 at the Leaf as proof. He only used a genjutsu reflection and a exploding shadow clone on Kurenai and a water jutsu and the MS genjutsu on Kakashi. He was worn out then and ran away.