I use a third party flash, similar to the SB-900. I had the same thing happen to me, and I know what caused it.
I was shooting group portraits with the camera on a tripod, using the IR remote to fire the pictures and I didn't wait long enough for the flash unit to recover between shots. So, I got one or two that were underexposed. I was too fast on the draw with the remote. My flash unit needs a couple seconds to recover between shots.