I found kind of an odd bug. first, the Garr7C and Twenty17 badges aren't saving for me, which isn't a big problem in itself because the cheat room exists. However, with the amount of badges I have right now, getting them from the cheat room activates the Waker fight, which I already did. For some reason, the green diamond that skips the fight does not work when badges are granted with the cheat room; it just resets the room. It does work when using the fast travel trophy though.