Qhimm, I've got a wild guess. Could it have something to do with the difference in file extensions? I mean, when you tried using Jenova to open the FF8 save files, could the program have looked at the file extension, then said, "Uh, no, this won't work"?
Or would that even apply? It sounds like you're mainly dealing with just the raw data, so I don't know if the file extension would have any influence on Jenova.