This is my second year photographing fall color in the Colorado Rockies. My first year was with Moose Peterson and this was one of the more important workshops I have attended. There are two factors you need to consider when photographing color at high altitudes and getting the color you see.
The first is heat shimmer. When sunlight hits a cool surface, the heat will ripple if front of your subject, especially if you are at a distance. This will make it difficult for your camera to acquire a proper focus and cause your auto focus system to jump around which will cause soft or out of focus images.
Second, the high altitude with the blue sky will wash out the color in your images, causing a blue color cast. The trick here is a higher kelvin white balance so moving to your cloudy picture profile and moving your temperature slider above 6000K.