The master switch is supposed to "vent" the vacuum when you lock/unlock the doors, so that sound is normal. You system is made up of a lock circuit (yellow/red lines) and an unlock circuit (yellow/green lines). There is a separate line (yellow/blue, I think) that runs from the check valve to the tank in the trunk. When you lock the doors, the unlock circuit vents through the master switch, and vice versa.

If you run the car for a couple of minutes it will pull a vacuum in the tank. How many times will the doors lock/unlock after the engine is shut off? Will the doors unlock/lock after the car has been sitting overnight? It's possible you have another small leak(s) someplace.