As first reported on Nikon Rumors, an owner and blogger Ming Thein had issues and sent it in to NPS. he got it back fixed and reports the following on his website.
Just got my D800E back from NPS. Apparently, the cause of the focusing problem in all cases is some inaccurate calibration data entered during the alignment/ calibration process. I was told it’s basically a case of hooking the camera up to the laser calibration jig, and letting a piece of software run a calibration routine point by point – there are no physical or mechanical adjustments made to the camera. The software then writes this somewhere in the camera’s ROM for future use. All testing is done with the 50/1.4, and the instrumentation is apparently sensitive enough to detect minor focus errors – they’re also present even on teles, but less obvious, is what I was told.
You can read his full blog here. So if you have this issue, send your stuff in ASAP for correction.