Fix'd by using version 2.312.
The problem seems to stem from being unable to open the Shiny Leaf drop down box. It's weird because I opened my Breloom that lacked these leaves on the new version, saved, opened on an older version, and in the Shiny Leaf menu 1, 3, and 4 were checked. Strange.
It's also caused by the inability to change the Game Met, and Game Hatch Condition from BW2.