This drove me nuts until I figured out what was happening. If you've already beaten a level, the game will only count the perfect in the stats if you beat your old score. If the expert threshold is $3,000 and on your first play through you got $4,500 then to get a perfect that counts towards the stats and achievements, you have to get $4,501 and not just $3,000.
If you want to go for the all perfects achievement (which I just got earlier today, woohooo!), I would suggest resetting the game data and going through again. I did this and just played the levels sequentially without moving to the next until I got a perfect.