As someone who provides commissioning services, I hear the above question on a regular basis when I lecture on this topic. The answer to the question has been addressed in Rebecca Ellis' column in the past, but quite honestly, I do think the client has a right to ask this question and get a "yes" for an answer.
After 38 years in this business, one thing that continues to remain the same is fair-to-good building control system performances. If you don't believe me, ask the people who created the LEED(tm) certification program, where commissioning is a prerequisite of these projects. They recognized that energy-efficient design on paper doesn't mean energy-efficient performance after the design engineer and the contractor have left the building.