The problem was that the installer was doing his first spray foam job ever, and the thickness of the insulation varied from zero (visible roof deck) to about 9". Unfortunately, good average thickness doesn't cut it. The coverage needs to be uniform because a lot of heat will go through the under-insulated areas. (See my article on flat or lumpy insulation performance.)
Spray polyurethan foam does effectly prevent all six of these heat transfer methods from occurring. These should be the mechanisms by which you judge insulation, in addition to their R-Value. If you're uncertain about installing spray foam insulation, Energy Star has a map that recommends levels of insulation by R-value and cost-effectiveness in the United States.
Sean, thanks for jumping in and answering John's questions. About choosing the right foam, I intentionally avoided the open cell vs. closed cell foam debate. I did this partly because it's worthy of an article all by itself, but mainly I didn't include it because, despite all the warnings the two sides issue about the other, I've never personally seen a problem caused by using open cell where they should've used closed cell or vice versa. I'm sure things like that happen; I just haven't seen it yet.
Silicone based coatings can be spray or roller-applied, and should utilize a medium-nap roller when rolled. These coatings are applied anywhere from 2 to 3.5 gallons per 100 square feet, depending on the substrate. Silicone has two major advantages over the other four types of coatings that should be considered when searching for the best roof coating: 1) it can resist ponding water for extended periods of time and 2) it can adhere to most substrates without a primer. Because of these two major advantages, silicone is the best roof coating that satisfies both quality and cost-effectiveness.