Hi -
I think at the moment, the RGB LEDs are controlled via a PWM controller instead of a static voltage level (such as other single color LEDs) in the HDF file for BlackBoard Rev. D. With RGB LEDs controlled by a PWM controller, it is possible to output any color by specifying the intensity of RGB channels. You can refer to the following page about the register definition of the RGB LEDs: AXI PWM.
I think a more detailed documents on the new RGB LED control module is on its way.