David,
On the D300, the commander mode "TTL" fires the built-in flash. Commander Mode "--" also fires it, but at a very low output that has little effect on most photos. It must fire it because the built-in flash is the source for the IR trigger for the remotes. Try taking a picture of yourself in a mirror with the commander mode in "--", you can see the built-in flash fire in the picture. If you want to totally eliminate the built-in effect, you can simply block the built-in flash with your hand or Nikon makes a little flash blocking accessory that lets the flash fire and scatter, which will trigger/communicate with the remotes without getting any direct flash from it.
