Before you do anything, do a reset. Hold down all the buttons with a green dot next to it to do a reset. It'll revert any custom exposure, white balance etc settings to factory default.
you're shooting on 5.6 aperture and low ISO (220-250ish). Try changing the Exposure Mode Selector to P (Program mode), then use the front dial to change to the highest aperture ratio your lens will support (from the looks of it your VR lens goes to 3.6). The camera will then automatically choose an exposure and shutter speed for you to suit. Also try switching to RAW mode when shooting. This will allow you to fine tune your exposure settings in post processing.