You don't say if you are shooting raw or jpeg? If it's raw then they always produce flat images. The fact that it was a dull day will reduce the vibrancy of the image making the shot look darker. It could also be that the camera under-exposes the shots when you do close-ups. What does the histogram say? On my D3 I usually have it set to -0.3 or -0.7 I this give the best outcome in most situations.
