Here's my totally uneducated guess on what's really happening:
Nikon may have had an problem in a single FX assembly line, affecting initial runs of both D4 and D800/e bodies, and in particular, their AF assemblies. These affected units are scattered among US serial numbers, at least ranging from 3000XXX through 3007XXXX, as seen by reported SNs here. This may have been the pre-release inventory build for the initial product run, totaling approximately two-months of production, prior to launch.
Since the majority of these pre-launch bodies sat in a warehouse as the production line got up to speed, awaiting their official launch date, the bodies didn't see customers' hands for a few months. (It's difficult to explain, however, how their statistical sampling process [QA] missed this problem, unless they don't even test for this specific issue, which is more likely, if the QA is based on manufacturing tolerances alone). So, since the bodies remained in a static state in the distribution channel, no customers were available to "beta test" for this issue. My guess is that the number of affected bodies may run well into the thousands. And, that's why Nikon's silent on the subject--it's a brand-destroying marketing mess.
I think Nikon is quietly administering repair procedures (but why so selectively is a mystery), which are effective at resolving the problem, and is currently dealing with the logistics of communicating the correct procedure to its service centers, worldwide. The equipment, "special cable" for connecting the D800 to the calibration computer, as well as specific written procedures on how to diagnose and resolve the problem, all needs to be produced, acquired, shipped, and communicated to each service center. There may also be some internal friction causing some delay. Other than that, I haven't a clue why the repair process has been so uneven and disorganized up to this point.
