I'm using Desmume, the dungeon kept freezing so I started frequently saving after completing a floor so I wouldn't lose items. After I saved on the new floor the game froze again and then it returned me to the guild and counted it as a loss and wiped all of my money and items. I used the patch at the end of your post. 3.0.3 I think it was. Also, how do I get to the mega evolution stuff? I thought I had the game completed and found out there's so much more to do and I'm kind of excited about it now
Edit: So, it appears it was the randomizer settings causing the freezes and crashes. I turned it off to see if it fixed the issue and it did. I can't turn it back on now though, it says this menu isn't available to me no matter what mode I try to use. It's kinda not a big deal though as I've already recruited pretty much every shiny legendary/mythical before not being able to use it, and since I turned it off it hasn't crashed once.
Edit 2: it is the randomizer. I turned it back on and it started freezing again immediately on the first dungeon I went into, zero issues with it off. Also, I got a challenge letter from Mewtwo for the 40th floor of Sky Stairway and I've gone through the 40 floor dungeon 4 times now in the past day with various items like the dream catcher, secret slab, and holy lyre and every time I get to the end floor it just ends the dungeon. Without completing that I can't continue in the story and I'm not sure what to do. I've beaten rayquaza twice and gotten his exclusive item and the world treasure from him, and now nothing at all happens when I hit floor 40.