I'm having the same issue, even in borderless mode it freezes bad enough that I have to restart my PC. Going to try windowed now. Only started happening when I was about 3 hours into the game.
One time the game actually saved my progress, but attempting to load that particular save results in a
runtime error.
I have to say, the most annoying part (well aside from me having to restart my entire computer) is that sometimes the last save is several minutes away, so I've had to repeat some areas/puzzles a few times. I've started quitting to menu every couple of minutes in order to save my progress now, which works but is pretty annoying and kills the immersion. If only there was a simple "save" button :/