The high-scores are loaded at the start of the game and then saved each time you get a better score (after entering your initials). Something wrong with this?
It is not clear to me where the problem is. As I said, the scores are loaded at the beginning of the game and saved every time you get a better score, so the scores are always updated both in memory and on disk. However, keep in mind that there is a separate ranking for each selected Layout. Could this fact have misled you?