I'm also using an EverDrive (the EverDrive-GBA X5 mini to be precise). In case it's relevant: I had the Debug menu enabled and I used it to edit a few of my party pokemon. I edited the level, IVs and some moves. I don't think I've used any other feature of the debug menu. I'm playing mostly with vanilla settings, though I had my starter Pokémon randomized.
I've attached the corrupted savegame and an earlier one that's still intact, maybe this can help you to track down the problem.
Edit: oh, I also had graphic glitches on the summary pages of my party Pokémon from time to time. But I just ignored those.