it sounds a bit different from your probelm but i seem to have something similiar. save files won't work (both loading and saving) and game freezes at the load screens. i thought it was solved by running steam as an Administrator. the game would work for a bit (10-15 mins i think) and then ,again, i can't save or go through the loading screens.
i figured partial workaround that lets me keep playing for few more minutes at least until i need to apply it again.
everytime the game starts, it creates the folder: \Users\[user Name]\AppData\Local\Temp\Obsidian Entertainment\Pillars of Eternity.
inside it there is a folder named "TempSaveData" and a zip file named "loadedSave".
some time after i start the game the folder would get deleted . after the folder is gone the problem starts with the saves and the loading.
in order to be able to keep playing i just copy an empty "\Obsidian Entertainment\Pillars of Eternity" folder i made outside the temp folder (the files that were there when starting the game aren't needed). that lets me to keep playing without any problems until the folder is deleted again.
the game puts a screenshot.png file in there when i save and deletes it right away.
that what is causing the crashes for me but since for me the game at least works for a while at the start i'm not sure if you are having the same problem.
i hope it helps someone at least.
