Did you actually see them replace all the parts that they say they have replaced and did you see all the old parts?
Did you supply all the parts ? if so then they may use that as an out.
I would make them aware that you have "noise" issues and make an appointment for next week so that they can inspect your car.
In the meantime put some miles on it over the weekend to allow everything to bed in, however I suspect that they will have to pull the box again.
Alex.