Yesterday I received another answer from Nikon customer service concerning the problem with the CLS system (triggering flashes wirelessly that is).
Recap: During a shoot I discovered that the internal popup flash of the D800 won’t trigger the slave flashes reliably. Sometimes it triggers, sometimes it doesn’t. I wrote a message to Nikon and got the reply that they tested it with four D800s and could not reproduce the problem. I sent them a picture showing the three flashes I used. On one picture the flashes stayed dark, on the other they were triggered.

Today Nikon gave me instructions on how to send in my camera for closer inspection. They can’t reproduce the problem or analyse it from the disance.

I am reluctant to give my camera away. This will mean 1-2 weeks without it and I still hope for a firmware update which will fix the problem.

On the other hand I probably should not be such a terrible pussy and just send it in. I still have the D300s and it served me well over the years, producing countless excellent images. Not having the D800 for a short period of time is not going to kill me.