My first DSLR was a D80, and I believe when it first came out there was a lot of debate about it's metering system over exposing.
It seems Nikon tweaked the matrix metering on the D80 making it behave differently than any previous model. As such many people dialed in a constant -.3 EC to prevent it.
In fact a funny ancillary story is that when I bought my D80 and the sales person knowing this was my first DSLR set it up for me. He let me watch and explained what he was doing, but did it so fast I didn't know what he did. I then joined Nikonians and was puzzled by all the over exposure comments being that I didn't seem to have the same issue. As I read the manual and started playing with the settings, it's then that I realized he had dialed in a -.3 EC.
Of course if you switch to spot metering you should not have the same issue.
#3. "RE: D80 overexpose" In response to Reply # 2 Sun 01-Apr-12 12:41 AM by elec164
I never really use Green Auto or any of the scene modes for that matter. Using Green Auto mode should not affect metering. But it will affect the way the image raw data will be processed to create the JPEG.
Any of the scene modes or the Green Auto mode have their own preset parameters that will override certain user selectable ones. For example it puts you into sRGB even if you have Adobe RGB selected.
So what appears to be an over exposure could in fact be more of aggressive PP.
If you have an NEF to work with it might be possible to tell if it was actually an over exposure, or overly aggressive processing.