This is a hardware limitation of GPUs before the GeForce 600 series, not a software bug. Even when no 3D programs are running, the driver will operate the GPU at a high performance level in order to efficiently drive multiple displays. In the case of SLI or multi-GPU PCs, the second GPU will always operate with full clock speeds, again in order to efficiently drive multiple displays.
GeForce 600-series and later cards are not affected by this limitation.