I received my D800 body back last week from repair attempt #2. Melville turned it around very quickly, during Sandy no less, but...
Executive summary: Still not fixed.
I tested my 24-70 mm F/2.8 and 50 mm F/1.4. They both exhibit the problem still. I used FoCAL to look at the AF fine-tune. There's been some change to the center focus values. Now FoCAL is recommending values around +10, whereas before it recommended around +18 or so. So they did something.
However when I compared the left and right focus points, they aren't consistent with the center. The left focus point is very close to AF value of 0. So it really looks like they just set it up so that would work.
I'll spend more time testing more lenses, but it seems clear to me that Nikon hasn't figured out how to fix this problem for some of our D800 bodies. At this point, I plan to use it with the center focus point for the next couple of months and see if they've gotten their act together.