Wow I'm surprised no one has responded. I was about to ask the same question and came across your post. I just got my D800 a couple of days ago and have noticed the rattle coming from the flash area. I went back and tried the same thing on my trusty old D80 and nope, solid, no rattling.
I'm wondering if my D800 is like your first one. Mine really makes a LOT of noise. Even moving it slowly I can hear the little pieces inside move like a couple of lose screws rolling around inside the body. At first, I thought it was the triangular hooks for the neck strap moving around, but after holding them still, it still makes noise. Flash up, noise gone. Like you, I feel the same way. I might expect this on a $200 camera, but $3k, I expect it to be solid.
Has anyone tried tightening the little screws some on the bracket for the pop up flash?