Craig: Yes, that's the issue. I've seen it , too, and so far I have found no way to get a button programmed to [AF Area Mode]+[AF on] ->3D to get reliable 3D operation if the default AF mode is Auto or one of the wide areas. It works if in subject detection mode and a subject is detected, but not so well if at all if subject not detected. I can't understand the folks who argue that with subject detection so good you never need non-subject 3D. What about landscape when you want to focus and recompose on a flower? Or chasing a butterfly the system doesn't recognize as a subject? Or elephants when you want to focus on the eye? Anyway, something odd is going on and I hope Nikon recognizes it and fixes it.
Well, I have many many times where subject detection doesn't work, though with recent firmware changes it sounds like the size of subject detected gets smaller and smaller. That's a good thing for me as I often shoot with subjects at the limit of various ranges. (And crop..)
But here's the thing that I think makes the whole thing go away for me and a lot of others. Set the 'right' thing when pressing the AF button on the side of the camera. Set it to 3D. (Or pinpoint ?)
Now, if you are like so many of us, disable AF from the shutter release. Now set any of the non-shutter-release buttons to whatever AF settings you want, and I think they work fine.
I think - please correct me if I am wrong - that the only function of setting that setting when you press the AF button on the left front of camera is to set the shutter release button's AF function. (3D, Auto, Dynamic, etc.) If you disable AF from the shutter release, I think all this works as expected.
But it does feel like auto-something is bleeding into the 3D tracking otherwise.