Hi Craig There might be something else wrong with your camera besides the focus - the metering perhaps? Please look at this article by Thom Hogan: "I'm concerned about the quality control on the D800 models. Some of this has to do with bugs in the firmware (I found many, several of which I reported to Nikon, one or two of which have been fixed in firmware updates; eventually most if not all should be fixed). I don't remember a Nikon model in which I've encountered so many unexplained problems as I ran the camera through the paces necessary to write my Complete Guide. At least once I triggered an ERR condition on my D800E, even though I don't believe that there was an actual problem with my camera (hasn't recurred, and I was doing some abuse testing of Live View and menu interactions at the time).
Meanwhile, we have numerous reports of focus issues, in particular left AF sensor problems, which I've verified in at least two copies of D800 models I've examined. Nikon now has a redone test and correction procedure for dealing with cameras with this problem, but if you encounter it your camera will have to go back to Nikon for the fix.
Finally, on my D800 some AI-S lenses don't index the aperture correctly and report an FEE error, while my D800E has no problems with those same lenses.
In sum total, I've personally seen and heard from others of enough cases to come to the conclusion that this isn't the level of QC I expect from Nikon, especially for a US$3000 camera. I seriously hope that my sample is skewed and that there isn't a decline here, but I do note that real D800 complaints seem to be prevalent on pretty much all Nikon-related sites at the moment. So my recommendation is this: don't be afraid of those reports, but also don't rush off to a critical shoot with a brand new D800 model before you've seriously put it through its paces and you're sure there's nothing amiss. Trust, but verify."