I know you said it is a real copy, but it is possible you have a fake copy (and you just couldn't tell), and Checkpoint extracted the data from the correct partition. Except it would only be accurate if it were a real game, hence why correct partition but wrong file.
Also, if you 'restored' this bad file and yet you were able to progress the game, it just sounds like your save is somewhere else.. As tho your save isn't in the common save partition.
(and the reason why the file of a different game exists is.. maybe someone did a crappy job and tried to overwrite a game or something, who knows)
But yeah, try with TWL save tool and see what the result is. I know sometimes people have issues with Checkpoint, and TWL save tool seems to go around that.