The D3 LCD is supposed to be calibrated. Whether it is or not, what you see on the LCD is determined by the settings of the picture controls -- the current JPG settings. If you want it to accurately reflect your RAW exposure data, you would want to sent the picture control to "neutral" which is the linear sensor capture. This way, the histogram will accurately reflect the highlight exposure, and the colors will not be affected by any tone curve. Keep the saturation, contrast, sharpness settings off to avoid further artifacts. I usually set LCD (as opposed to picture) brightness = -1 in order to give me a better indication of the true brightness.
Does this help, or is the problem elsewhere?