I know that back in my D70 days, Nikon's meters were known to underexpose by a little more than 1/3 of a stop. There was a guy that created an in camera curve you could load that compensated in the shadows and mid-tones without blowing the highlights. Check out this page for some information:
http://www.planetneil.com/tangents/2...custom-curves/
If it was working well for you before and has only now changed, then I'm at a loss. You're on the right track with a full reset. It that fails, then perhaps a repair is the answer...
You wouldn't happen to be photographing scenes with a majority of lighter tones, would you? When you go from winter colors to summer, your meter will try to drive them to middle gray, which will show up as under exposure. The wedding photographer's nightmare of black tux and white dress come to mind...