FF6 Advance Hacking: Event Trigger Problems?

I was wondering, has anyone here tried to edit the Advance version of FF6 much? And if so, did you then have any problem's in the Dragon's Den? Or really, anywhere else, with events not triggering correctly?

I made a small romhack with FF6Tools for my own amusement....
Really nothing major. I replaced a couple sprites and "job titles" and I used a hex editor to change some sprite palettes. I have another thread here in this forum detailing that fun. Probably right below this one.

I went to the Dragon's Den and fought the first dragon, the Ice Dragon. After the battle, it said the Ice Dragon was defeated, and then did the thing where it shows the blocked off areas and says "the barrier has been destroyed" or whatever...
But the Ice Dragon and the barriers remained on the map, and completely impassable. Therefore I could not continue on.

Sometimes switching parties would glitch the screen and render it impossible to move, and you would have to keep switching to get it back to normal.

I also noticed that in the Coliseum, there was a piece of magicite in the middle of the room that could not be picked up. It feels like somehow everything that relates to events got messed up, and I didn't edit any of those.

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.

I'm using a save game from GameFaqs to test this stuff, and I can confirm that the save game works perfectly fine on an unmodified ROM. None of these issues occur, so its not the save.