@BjFinest34 - You'll notice that one line that reads "if !attacker.hasBypassingAbility". That's from code left from copy-and-pasting code from a move effect. It's checking to make sure that the Pokemon who lowered your stats - which should have Intimidate since that's how this subroutine was triggered - doesn't have Mold Breaker. Unless you've completely recoded your game to allow Pokemon to have two abilities, this should never ever be false. Just change that line to say "if true"
@Sharazel - Okay. I see what I did to fix this. Search for "def pbResetForm". There you should see a list of Pokemon who have in-battle-only non-Mega forms - my game has Castform, Cherrim, Darmanitan, Meloetta, Aegislash, and Chesnaught (your mileage may vary, and you very likely won't have Chesnaught). Add lines of code for Kyogre and Groudon (and any other Primals you have).
@Sharazel and Vanillabrocker - I could never figure out what the problem was with the Gen VI Pack and the Pokedex's forms page, but yeah, it's there. I ended up recoding the main page of Pokedex entries to change the form of the image if you press Q and E (and also show female sprites if you press E, or Pokeminorities if you press A, S, D, or Z), which also allowed me to show the types of both Delta and alternate forms. But in order to do that, I had to extensively recode certain parts of the PScreen_Pokedex, Pokemon_MultipleForms, and PSystem_Utilities scripts, since what I end up doing is making a hidden variable that is a fully-fledged Pokemon and altering it to fit certain criteria, then asking that Pokemon "what type are you?" and displaying those types rather than the ones in Pokemon.txt