The issue is this, which has apparently been a very long-standing issue I myself have only recently experienced for the first time since buying a Nikon flash: When the SB-910 (in my case) flash AF assist is enabled AND the flash AF assist lamp fires, my Nikon D800 camera will ALWAYS focus inaccurately or push the focal plane at least -15 microadjustment points back versus when the flash AF assist lamp does not fire. Since the AF assist lamp only activates in AF-S mode, the issue only occurs in AF-S mode.
In my case, my 35mm f/1.4g focuses accurately with NO AF assist lamp, or using the camera's built-in AF assist lamp, using about -5 microadjust. If my SB-910 is mounted, turned on, and the flash's AF assist lamp activates, -5 microadjust ALWAYS results in severely back-focused images. When the flash's AF assist lamp activates and I have the camera set to -20 microadjust for the 35mm f/1.4g, then focus is ALWAYS accurate (as long as the target is lockable). Several people have tested the results when covering the AF assist lamp, and the result is roughly the same as when the AF assist lamp is not covered.
Reports of this issue with previous cameras and flashes have existed since long before the D800 and SB-910 were announced. However, the most glaring and frequent reports involve the D800. The issue apparently is not experienced to the same degree by all persons, and a few have reported not having the issue at all.
The only solution ever suggested has been to turn off flash AF assist, which is not a real solution because it does not provide the advantageous flash AF assist lamp that is half (or more) of the reason to have an on-camera flash in low lighting. The built-in camera lamp is both intrusive to subjects and not very effective at even moderate distances, and the camera often will not be able to lock accurately without any focus assist. This is a workaround, not a solution. There needs to be a solution.
Some persons have reported not having this issue with the SB800 or with different cameras (sometimes different model, sometimes same model) in combination. However, some have reported the issue with SB800 as well.
I have posted on another forum a compilation of the links I have found related to this issue so far. This is the first day the list has been up, and it continues to grow.
Please keep this topic alive. This is a long-standing, widespread (though not universal) issue people have been encountering for years with at least two generations of Nikon cameras and flashes. Not everyone has the issue with the same combination, but those who do have the issue need to share it with the outside world. I am making a point to expose this as the larger scale issue it truly is. We deserve to have the flash focus assist lamp work properly and not cause a new problem. Nikon needs to resolve this problem by correcting it, not trying to hide it under the rug. They never publicly acknowledged the widely-reported D800 left-side AF issue that many users (including myself) had, and they only acknowledged the D600 oil spots issue immediately after a class-action lawsuit was announced and China had publicly denounced the Nikon D600 camera issues. What will it take for them to do the right thing?
A company with a repeating show of unethical behavior demonstrated by all of these recent issues that they ignore and/or deny the existence of (until a major country denounces them) will very likely develop a negative stigma over time. That stigma could do far more damage than the price of some additional effort to acknowledge and resolve issues and keep the highest reasonable percentage of satisfied customers possible.
I am a long-time Canon user who has grown frustrated with some flaws and deficiencies in recent Canon products and have started trying out Nikon products because of that. I want Nikon to be a viable competitor and alternative, but issues like this make it extremely difficult.