I think I get it now. In other words, it appears MGS4, unlike most games, creates two seperate files in your Saved Data Utility folder. One being the actual "Game Save", the other being some sort of "System Save"?
Looking at the actual file names, that seems to be the case at least:
- BLUS30109G48510DF8 = MGS4 Game Save Folder
- MGS4.SAV = Game Save File
- BLUS30109S = MGS4 System Save Folder
- MGS4SYS.SAV = System Save File
Come to think of it, this is the only game I can think of that does have a seperate "System Save" file. I wonder why this is the case.