Nice solid game! It seems the high-scores are only loaded upon start-up, and not immediately after the initials being entered when getting a high-score?
edit: oh wait, I see I have to press F1 :)
edit 2: oh no... that removes them! :)
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?