Road bikes and Mountain bikes are measured differently. The size of a Cannondale road frame is measured from the center of the crank to the top of the top tube. I verified this from my own SR 500.
Mountain bikes are measured from the center of the crank to the top of the seat tube. However, I've seen this measured in shops using two slightly different methods. One way is to take the measurement holding the tape against the seat tube. The other is to hold a level at the top of the seat tube and run the tape straight up to the level from the center of the crank. I don't think there's much of a difference between these two methods.