You say that only because you have a Nun obsession!
How did you get all perfect but still not beat your high score?
This game confuses me sometimes.
Score in this game is not based on how well you do (well it is, but only loosely). Notice how the skill for all your rares is stuff along the lines of "Score increases by 180 with 36% probability whenever Perfect is reached 12 times."
Obviously, this means you can score higher on a run with 10 greats and the rest perfects than a full perfect run IF you get lucky with the skill proc's.
It's kind of frustrating, to be honest, but it's just a method built into the game to keep you playing (after all, you might get a better score next time due to randomness).