If your computer is doing anything else at the same time, it is going to slow down. If you were copying files, surfing the web, or even if you click on the finder and the program was running in the background.
There is a utility that you can use that is in your Utilities folder in your Applications folder called CPU Monitor. There is another utility called Process Viewer that allows you to see all of the programs that your CPU is required to handle at the same time.
Run the benchmark again with the CPU monitor visible. It should max out the bar.
With Process Viewer and the CPU monitor (with the expanded window) applications open, I ran the quickbench.app in 2.333333325 minutes. The Quickbench.app used an average of 92% CPU the entire time (the rest going to other processes) and only dropped as low as 84.8%. It dropped this low because the Window Manager was using about 8.9% and the loginwindow used 4.5% (why I don't know) plus the process viewer took about 2% or so.
Hopefully this helps you out.