I am aware of all that. Why I said when I play without a mod, it is a clean install. The save used never had a mod used with it. And I still get broken saves.
I have issues with EVERY release. modded or not. my saves never work.
I have to start new EVERY update. every once in a while a save from 2-3 releases behind current will load, but its not even worth trying any more. I just ctrl-skip past every choice to get to new content. I even made a freaking list of the choices...
loading a save either kicks straight to main menu or the last screen of the save and going either forward or backward also dumps to main menu.
edit: its not even update dependant. close the game, open the same install a week later and its 50/50 if a save will load or not.