Nice shot.
Were you using a polarizing filter? A polarizing filter darkens and enhances a blue sky the most when it's used in an area of the sky at around 90 degrees from the sun.
Whether you were or not, I'd imagine the bird has moved between shots further than you think and the amount of light scatter depending where your pointing your camera in relation to the sun can vary enormously, having a significant effect on colour saturation.
Edit
In fact if you look at the shadow under the wing you can see the first shot was far more into the light (toward the sun) than the second.