I wanted both the same screenshot, but both loaded differently, tho I guess this is fine.
First problem: I'm guessing that you're using Checkpoint in CFW EmuMMC, to dump saves from OFW (Stock Sysnand).
You're not meant to be able to do that.
Your Sysnand and Emunand delinked. You should remake emunand.
Second problem: How are you transferring the save to your PC. No reason it wouldn't open in PKHeX if it is updated
I'm guessing it's via FTP, and your transfer method is ASCII instead of Binary. OR, your PKHeX is not the latest stable build, hence why you couldn't open that save, and we could.