Did you try opening the load window and going through the save list? If the time was off enough when the saves were made that could result in them not being listed in the actual reverse chronological order.
I've just checked the list of saved games in game menu- they are all in the chronological order.
In the Saved Data in System Storage section of the Settings menu, is there any save data listed later than the timestamp of the latest save that shows up in-game?
All saved games are equal (in chronological order) in system storage, game load menu and even PS Plus storage... i don't know what is going on... i'll try to play one more time, save and take a screenshot, then i'll come back here.