Adam i can definately help with this one as I have the Nikon D800 as well.
Absolutely nothing wrong with your camera to start with, the built in mike is picking up your lens auto focus noise. 3 ways of stopping it
first = go into shooting menu-movie settings-microphone-manual sensitivity and adjust to a lower level. You should easily find your way from here to up or down sensivity, follow the arrow
second use an extrnl mike ontop of the camera ( this is a sennheiser MKE400) also i added a height extender to get the mike a bit further away from the camera. Another thing was with a short lens the dead cat might just show up along the top of the video as it did with my camcorder
Camera with extrnl mike (music playing to prove extrnl mike working). Here off camera on separate stand using extn audio chord
View: https://www.youtube.com/watch?v=ELGHuHKTNfA
without extrnl mike making same noise as yours. Notice focus change at same time
View: https://youtu.be/2iUVDwlu0MY
3rd way is to use manual focus only but that can lead to unwanted camera movement.
This should answer your question
Little bit more info
you will find wind noise excessive across the built in mike ,so much so it can ruin the video, my advice is to take the extrnl mike route, whatever make and fit a dead cat over it. Won't get rid of all wind noise but certainly helps
Ok why does this happen?
To me it is a design fault in the camera . the microphone 3 holes are right alongside the lens so no wonder it picks up every click of a lens
On close examination I found one of the holes was blocked as well so something to check for, I used a pin gently to open it up
Felt a bit like a dentist getting that shot
other camera was a Nikon D300 with a tamron 90mm macro lens and a cn-160 light and this taken quickly with my camcorder so DOF a bit out
