They usually either run the ride with the slowest wheel combination possible or the fastest wheel combination possible, and experiment with different wheel combos until they get it to an appropriate cycle time they like before handing the ride over to the park.
The sound as the train was cresting the lift was the anti-rollbacks going off. Kondaa has an anti-rollback wheel that keeps them up just like Skyrush, El Toro, Millennium Force, i305, and other Intamins have that keep them from chattering up the lift but they can still go off if the ride slows down as it is cresting or if the conditions are right.
Or in i305's and Skyrush's cases, the second they get wet they let the entire surrounding area know that they are wet and that they are not happy about it.
