I recently got my 5DII and I noticed the same thing this weekend. I think it is the result of using the anti-clipping feature in the Menu (sorry, I am at work and cannot remember the name of the feature). I noticed it when I manually activated the feature in the Menu, then dropped my exposure 2/3 to 1 stop to balance my dynamic range on high dynamic range shots (i.e., harsh light with bright reflections and shade in the same shot). This made my shots fairly dark. When processing the shots later, I brought up the darks and saw the color banding and muddiness in the dark regions. Your third shot captures what I saw in my shots.
Although the 60D is supposed to be an inferior camera, my 60D never demonstrated this pattern.