savestates still have nothing to do with it, and are fine as long as someone can save normally. furthermore save states can be legitimately used, precisely because of crashes/errors that can happen on Beta Roms, you can at least salvage the game. I've done that for many other hacks before, old or new. so you should not let "save states are cheaty" simply cloud your judgement.
also i had asked someone from another forum who had an old save file to check route 50 with the newest ROM, he had no issues, like you. seems like it happens on new games created on the latest ROM. probably events/scripts not triggered properly at the very beginning of the game or something.