SMC firmware is defective.
Apple knows about this, but they don't care. The only official GPUs the SMC actually supports are the ones that shipped with the Mac Pro. Flashed cards and even the 680 GTX (Mac Edition) can and often do cause whacky fan behaviour.
This more or less has to do with how the fans are throttled based on the power the card is consuming. The formula they're using for this isn't optimal for cards with their own cooling fans, so the increased power load causes the fans to spin up to unnecessary speeds.
Chances are good that if you "force" the issue by loading down the GPU (iTunes Visualizer, running a game, or an OpenGL benchmark, etc)- the fans will rev up, then start to settle down again. Once this happens, the fan speed should stay low until you power down the computer.
-SC