After finishing Episode 4 tonight I decided to reload the save and see the Penultimate checkpoint, where I got everyone, again.
Oddly this time I couldn't get everyone. So I checked my stats and found that the bulk of the choices were now being reported inaccurately.
So I coped the save into the other two slots and loaded up various points and indeed those wrong choices were being reflected in the story.
I really enjoy going back to my favourite scenes in games and so am really disappointed that in trying to do so for this game I've somehow completely changed everything that I did, simply by reloading the final checkpoint.
This is a truly fantastic series but this has really put me off from buying the final episode.