Pony Fantasy VI Remake

Quick summary of the mold problem:
I created new graphics for Air Force, Missile Bay, and Laser Gun.  When Drakey puts them in the game, Missile Bay and Laser Gun appear behind the Air Force instead of in front of it.

The biggest change I can see is that the original uses Mould 7 with the enemies in slots 0, 2,3, and 4, while the modified one has the enemies in slots 0, 1, 2, and 3, and might use a different mould.

I don't know much about Moulds - is there documentation on them somewhere, especially how they are stored? Is it possible something in the mould controls which slots appear in front of each other?