Hm, it’s weird, I’ve been able to 100% the game on the latest builds just fine - and I’ve confirmed with other people who have also been able to. If you’re missing 1% and you’re on the latest build then I can only think you’re actually missing something. Do you have all of the glossary entries unlocked? All of the scenes? Your tree is completely filled out?
When you said you redid the endings, you redid all 3 of the endings for both marion and jessie? Not just redoing one of them?