Professor Oak Challenge

A few days ago Retro Achievements launched a POC set for Pocket Monsters Ao and I started doing that. I had to restart my first try because I didn't catch a second Jigglypuff, that I needed to get Mr.Mime.

Anyway both in my first and now in my second try I had the same thing happen and neither do I have an idea why, nor did I really find any information on it online. I use Box 1 for Pokémon I still have to evolve, 3 for Pokémon that need a stone and 5 for fully evolved Pokémon but for some reason both times all Pokémon in Box 5 diappeared.

Does anyone have an idea why this happened? Is this a known problem in Japanese Blue? Might the POC patch cause that? Any information about this is greatly appreciated.

Some info that might also be important:

They were still there when I started playing about an hour ago, it happened at different points in the game with different Pokémon in the box. Only thing that was the same was the box itself.

Edit: Still in the second run and I've started putting the fully evolved ones in Box 4. As of now they're still here. Will update again if anything happens.