By layer I assume you mean layouts.
I have run into similar issues with my current project which also has three difficulty settings, fortunately a point is a point in my game the difficulty just affects spawn levels.
If I was trying to keep three separate high scores though I would make it easy on myself and use 3 separate global variables, one for each.
I would either have the layout add to the difficulty variable for its type or I would set the values of the other 2 variables to say 11 when the difficulty button was clicked and just never have my highscore display my score keeping variables if they are 11...