What is different when a CPU is operating at "turbo" frequencies?

Internal circuitry monitors the chip temperature and works out if it's safe to "overclock" the chip to the higher speed. If the system is under a light load and only one core is in use, there isn't too much heat being generated, and the chip can run at the higher speed, maybe doing only one task.

But if you load up the system with tasks that use ALL the cores, things will soon heat up, and the system switches back to it's true rated speed, the one that it can maintain reliably over the long term, even with full CPU use.

If they sold the chips as 3.9 ghz it would be false advertising, as they can't sustain that speed under all situations. They can do it under light load, or for a short period of time, but not under heavy use.

Imagine how you would be complaining if your "3.9" CPU was switching to a slower speed every time you started a game up? Where as if your "3.5" chip slows down to 3.5 under heavy use, you have no grounds to complain, because it's working as promised. Running at 3.9 sometimes is just a "bonus".