Yes this one is contraversial (sp?).
Many say it does not exist. Some (myself included) have witnessed it first hand.
All I know is when I used to use save and exit every once in a while I would get a corrupted save that would not allow me to continue. Either the game would ctd or an officer would be missing or some other goofyness.
It probably has something to do with system configuration (I have dual drives, (sh3 installed on D
dvd burner, cd burner, a couple of usb hugs blah blah blah). Im sure yours is different but you get my point.
All I know is once I adopted this procedure (save then exit manually) I have never had a corrupt save or ctd.