Upload & Sell: On
If I were you, I'd send it back for a replacement. It's certain that the 39pt cam 4800 is not as capable as the 51pt cam 3500, but the differences are not that great. I don't expect my d7k to focus as good as my d300 or d3s, but I do expect it to focus well under normal conditions. But, I have more faith in the AF capability of my d5100 than I do my d7k. As a general rule, all of my cameras are set to use AF-C, either single pt or 9pt dynamic, all of the time.
IMO, there are some d7000 bodies out there that are just wonky. I think it's just a matter of poor QC at Nikon, because there are too many folks that aren't having issues with the d7000. If you can't get a repeatable result, that's an indication of something wrong. Of course, that assumes your testing procedures are okay.
Maybe if you exchange it for a new camera, you'd get a good one.