Thanks for taking the time to look into the file!
Well, this is all very strange to me. I was looking carefully at the Pókemon, and most of the ones that have been marked illegal have my name as the OT. Which is very strange, because I didn't breed all of them. A lot of these are direct trades that I just threw in the box. I never tempered with these Pokémon, never edited them (I also didn't even have the means to up until two days ago, when I homebrewed my 3DS).
Well... too bad then. Guess most of these aren't good for much then...
Thanks Poke J!