Matt, there's nothing wrong with your calipers. At least, when I had the car there was nothing wrong with them. I've seen the stock BMW calipers go wrong, but usually it's when someone tries to grease the slide pins. And then the symptom is the brakes get hot because they aren't releasing fully.
When I had my ZHP I had the same problem with the brakes (occasional pulsation). I believe what causes it is not enough hard braking events. I never found a better cure than an occasional full-panic-braking stop from freeway speeds.
The Mazdaspeed suffers from this occasionally as well. It is what it is.
