FF6 Advance Hacking: Event Trigger Problems?

Could it have to do with the message that comes up when you load a ROM in FF6Tools asking if you want to move data in the rom around? Or the method in which I saved the ROM? I don't think the hex editing did it. Of course, I do plan to experiment and try to figure out what part of the process got things fucked up, but I was hoping somebody here might know something already.

You could try just moving the data with FF6Tools and see if those problems are present.