I'm not kind of expert or a dev of pkhex, but have you guys tried to import the latest working savefile, then make any edit ON THE GAME with the latest patch (like change a move, healing pokemon ecc.), backing up a new save file, edit it and then re-injecting it into the console?
PkHex is working great for me with a save dumped from the patched game.
Also, have you updated the game via official channels, or have you installed it via NSP / other methods?