I did a few basic tests. I set up 5 AA batteries on a diagonal, about 1/2" apart. I put my D4 with a 200-400 VR2 on a tripod, about 10 feet away and tried a series of three shots each at different apertures. First I used live view and magnified it to get a good focus on the middle battery. The I shot the image, then I switched to AF and shot another and then I moved the focus considerably and used AF to let it focus and shot the third of the series. All the images looked good and the focus seemed to be all on the middle battery. Depending on the Fstop, you could see some of the batteries in varying degrees of being out of focus.
I then put on the 1.7 teleconvertor on the 200-400. I repeated the series of shots. Everything looked good.
The next day I went outside and shot some moving cars about 500 - 600 yards away. Everything focused properly.
Nikon asked me to send them the original files of some of the bird shots that I had take which were out of focus (yet showed the right focus point in viewnx). I did that this morning and am waiting for their response. It's amazing how slow they are to responding to email issues.
I hope to hear from them tomorrow. Maybe they can shed some more light on this problem. I will probably try to do a few more outdoor bird shots later this week and see how they look.