The game was made in the Japanese version of WolfRPG Editor. If you're editing it in the English version then I don't know what else will cause issues / change. There is definitely a bug in the way the Japanese version of WolfRPG Editor was compiling it, as I said in my post.
The SHA-256 hash showed technically 3 files changed, but it was the Game.dat file causing issues. I reproduced it multiple times, it is definitely the issue at hand.
If you figured out another way to make it work, cool, but like I said, it doesn't matter.
1. I'm waiting on DreamSavior to finish his new engine.
2. I have it working for the third time.
Edit:
I'm not trying to be an ass about it. It's just annoying to me to beat a dead horse when the problem is solved.