No breakin. But they will sometimes trap a certain amount of air that can take a day or two to work out - although this is rare and generally doesn't "hum."
There may be something sitting against the pump or motor which can be moved: ozone system, tubing, power cord or similar.
If none of these things help, the dealer can replace the motor: what I mean is that the Watkins Warranty does in fact cover a noisy component.