If I go to the PC in the game, move some Pokemon to other boxes and then save and load the file in Pokegen, it shows the Pokemon in its original positions instead of its new ones. Pokesav shows the Pokemon in its correct positions.
I can upload a save file with this problem if you need it. I'm fairly sure this wasn't happening with Pokegen 3.0.5
A save file. It seems to happen in other circumstances as well. Look at the attached save file, box 18. A recently captured Pichu should be in position 9, but Pokegen shows it empty. Pokesav and the game show it is there.
No, I'm not using "Ignore save file checksums". I have edited the file with Pokegen and Pokesav (item editing before you added support for it), but I haven't manually edited the file (hex editor, etc...). It's a bug with the new versions, as I have found a copy of Pokegen 3.0.5, loaded the save file with it (I attached the save file to my last post) and the Pokemon is shown in box 18, like with Pokesav and in-game PC.