I had the same issue : -20 (or +20, I don't remember) with my brand new D800E on a just-re-calibrated Nikon 24-70 (it fell HARD and had to be repaired). To make things worse, with most lenses, the focus results I was getting were simply unpredictable.
Standard AF was visibly sub par compared to LiveView focusing. To put it in less words: AF was completely broken and unusable, on any focus point.
Nikon took back the camera under the warranty with no discussion. They then took their sweet time (5 weeks...) but when my body came back, micro focus was perfect at 0 on my 24-70, using lens align for reference. And the culprit was the body: I hadn't sent the 24-70 with it.
Now, why on earth would they sell a non-calibrated body in the first place, that is the question...