I'd like to point out I"m also encountering this. If I try to save manually, overwriting one of my old saves, it brings up the dialog box, then clicking "Save" behaves the same as clicking cancel -- it does nothing, closes the window. Latest patch has not fixed this. I have noticed that if I re-load an earlier save, I'm able to overwrite again.
From searching the forums I've found a few other threads reporting this, clearly a real bug, please attempt to resolve, thank you!