I boot it up, set the configuration correct, boot up the game, hit continue, and my regular save is back.

So I verify the integrity of the game cache on steam and it re-acquires two files. So I fuck around with the configuration and no matter how many times I do it, nothing works, even though when I usually do that it works. I forget the exact wording, but it's something like that. Remember how last night my save reverted to an older version? Well, when I was booting up the game today, it gave me the usual 'the configuration doesn't match this PC's set up' error message.