I will give you possible answers to your other complaints as well now that you got me going.
Your target was not moving. but what about your hands? Did you shoot all these shots on a tripod? or handheld? Was it the same scene? with the same contrast in your target? Was the light conditions the same? An accurate conclusion can only be made if the test is done in a controlled environment. tripod is a big part of that.
This I have already shown is user error.
Flash metering and camera metering are two totally separate metering sytems. You need to read up on how i-TTL works. Whether the flash is on or not, has no bearing on the metered exposure from the camera. Do you need proof for that? I can give you many links to this as this is well documented. Or you can google on your own.
What was your metering mode. What was the scene like. What was underexposed and what was not in the scene. No details, no samples. What can we say? You cannot depend on the camera meter to nail it according to what you desire all the time. It is the same in the D90 either, same in the D300s, same in the D700 and same in the D3s. The meter is a result of what the camera thinks is the best exposure with the parameters it was supplied with. But the photographer have to determine what should be the final exposure be. That is what EV compensation is for.