Nah... he is actually shuffling well. He just always tosses a chunk (from the middle) to the top each time before he mash shuffles. It's actually a very effective method of shuffling and is actually better than only mash shuffling. No noticeable shenanigans there.
With leyline in play, other players can still target your graveyard, just like they can target your creatures. Leyline only stops spells that say "target player."