Just to clarify, when you load a slot from the second playthrough, it's loading the first playthrough? How long ago did you begin the second 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?