In 1.9 the dragon always dies on top of the portal, meaning almost 100% of the time the Dragon Hide falls into the portal, going to spawn. My solution/suggestion is either make the hide go directly into the the player's inventory, or have the hide float in the air for a couple seconds like the Dragon Heart from Draconic Evolution.

The Ender Dragon Scales spawn right where you kill the Ender Dragon. so that means if you killed the Ender Dragon over the portal your Scales are gone.