The other day I was shooting some portrait head shots with my D700 popup flash and a SB-900 fired remotely. I was really surprised to later find that my subjects had a 2nd catch light in each eye. It didn’t take long to realize that it had to be coming from the popup flash, even though I had it turned off in the commander mode settings in the camera.
So I did some research and found out that this is the case with the popup flashes (D200, D300 and D700 at least) when used in commander mode. However, I did learn along the way that while the SB-800 will also do this, the SB-900 doesn’t (when used as a commander flash from your hot shoe).
Anyway, long story short, I had the solution to this problem all along – it came in my R1 macro speedlight kit. I didn’t get the R1C1 which comes with an SU-800 – which would be an even better solution, but it did come with a Nikon SG-31R IR panel (get one at B&H). This little unit definitely seems to solve the problem without having to spend the money on an SU-800, or a set of pocket wizards (which I’ve love to have of course). I haven’t done any serious testing yet to see if using this thing will still fire a flash inside of a softbox, but from what I’m reading it definitely should work.