Did you look in the secrets menu (in the extras section)? I hope there hasn't been a misunderstanding - bitter end and all's well that ends well are achievements that unlock bonus scenes, they don't change how the storyline progresses in the main game.
edit: I looked over the code and still have no idea what the problem could be, especially since it works for most players. If this isn't a misunderstanding on your part and you'd like to discuss this more closely to hopefully help me figure out what went wrong, you can send me an email (viscereyedev@gmail.com) or message me on Discord (RA111N#8101).