This is normal if you don't have VSync enabled. What happens is that without VSync, the 3D application will render with hunders, even thousands of frames per second (FPS). This stresses CPU and GPU to their maximum. Even glxgears without VSync eats 90% of one core here (and runs at 5000FPS). Enabling VSync fixes the problem.
This is by no means a Linux problem. Exactly the same applies to Windows and other systems.
You can enable VSync in Catalyst Control Center if you're using the binary drivers (3D->More Settings->Wait for vertical refresh->On, unless application specifies).
If you're using the open source drivers, you might be able to enable it with the "driconf" utility.


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