I would suggest you need to:

1. Do an AWFUL lot of reading up on how incident metering works, and
what the pitfalls are. I presume you have done this sort of stuff
before? If not, then it's probably a technique issue, not a camera
issue, and you would be better served to trust the Nikon's metering
until you get incident metering sorted. Bear in mind that
'out-of-the-box', the Nikon is probably set up to give over contrasty
results with occasional blown highlights and its dynamic range is not
really state-of-the-art anyway - if you are not dealing with those
issues, incident metering may not be such a good idea.

2. Check the Nikon's exposure settings against a couple of other (pref.
non-digital) cameras that you !know! have accurate metering, or get it
checked at a pro photo store - tell them what you are trying to do.
It's possible the Nikon is simply not telling the truth about its
settings, be that shutter speed, aperture, or even ISO..