I'm loading from my second playthrough, which I started a few days ago. I saved and took a day or two break from the game. The game updated during my break. Also, and I don't know if this is also a factor, I overwrite the same save slot that I used in my first playthrough.
So when creating new saves, you are seeing that the new saves are there with a new date and time, but when you load them, it's loading a much earlier save?
I'm wondering if the slots are somehow getting mixed up. Have you tried it with both quicksaves and manual saves? If so, is it happening for both?