Well, it still does happen without fail on saves before choices, no matter the chapter. It happened repeatable with a ch. 16 save, one from 7, one from 3 and I was too pissed off to try the rest!
That is very weird. I just tried to replicate it several times with every save in chapter 3, one by one, and I could not make it happen once. I saved on every message
In my testing, it was always tied to the end-of-content message. Even now, I can load a save near the end of the game, push forward to the end-of-content message, load another save, and have the choices break. Afterwards, loading any other save no matter where will also have broken choices. From there, if I restart the game and load a save before the end-of-content message completes, the choices work again.
And frankly, I was checking grammar for the entire game, so I had to save on almost every single choice to check both sides for any mistakes. I must have gone through hundreds of saves, it only ever triggered when the end-of-content message was in play in Chapter 18.
To be clear, when you say it happened repeatably with 16, 7, and 3, do you mean you triggered it once in 16, then tried loading 7 and 3? Because that's very different from triggering it in 16, restarting the game, triggering it in 7, restarting, and triggering it in 3.
Send me the files if you have them please, I'd like to take a look.