I have a D200. It is set up for auto flash. Nothing unusual in its settings. But the photos are always over exposed, by quite a bit, at least 2 stops. I tried it again with the SB-800 and the results are the same.
I have a D70 with built-in flash and I do not have any flash problem.
Make sure you don't have flash compensation dialed in. Press the lightning bolt button just below the button that pops up the built in flash. It should show 0.0 in the control panel. If not rotate the front sub command dial until it reaches 0.0.
A lot can depend upon what your subject is wearing and the background. A large area of white/light color or black/dark color can confuse the metering systems of the camera and flash. Yes, there are two exposures computed, one for the ambient light and the other for the flash.
A sample image might help us see the exact problem and help to explain what happened and what you would need to do to fix the problem.