I've had problems with Nikon D3 exposures myself and they all seem to be centred on the one lens, a 24 -85mm and although it usually works well there is no guarantee you'll get the exposure you were expecting which is a bit of a pain as it's the one I use 90% of the time. A forum member kindly suggested that it's a matter of fixing the contacts but I am rather heavy handed so have left well alone for now. I do wonder though whether it might not be a genuine lens, it has a serial number alright and the box etc, but that's still no guarantee. The two longer zooms (one a Sigma) seem to be fine with hardly ever a problem that's not due to my incorrectly setting the camera.
When the camera starts making a series of mistakes in exposing I find that returning it to factory settings seems to clear the bind that the body has got itself into (assuming it's not just the lens).