I have had the same issue for over a month now, anything after 1.4.1
I have the Steam "Performing first time setup" bug, so I use the run native.exe as administrator workaround to launch the game. Now, all save files are saved as 1kb .tmp files OUTSIDE the Game Saves/Native folder. I have reinstalled, verified, do not run mods, have no anti-virus, cloud, OneCloud or microsoft issues. Updates since July seem to be lacking the steps to save correctly when running through native.exe. The game is unplayable after 1.4.1