The setup was perfect: SB800 set to "Remote, Group A, Channel 1",
D800E set to "Commander mode, Group A (TTL), Channel 1, two second shutter time, rear curtain sync."
The popup fires once when the shutter opens, but the remote SB800 does not respond. Just prior to the end of the two second shutter time, the popup should emit a second "fire now" pulse. It does not appear.
In Commander mode, the small lightning bolt symbol does not appear in the Control Panel, or the Information Display when the popup is set to off (---), unless I push and hold the Flash Mode/Compensation button. This is apparently to indicate that the popup will not fire while the shutter is open, except for the low-power "Fire Now" pulse necessary to trigger the remotes for image capture.
The lightning bolt symbol appears in both locations when the popup is set to other Commander flash modes (Manual, TTL), without pushing and holding the Flash Mode/Compensation button.
I tried a couple different SB800s and an SB700 (I have twenty Nikon speedlights, including twelve SB800s ...) with the same results. I tested the SB800s on other cameras and they worked perfectly in the remote mode.
In the store yesterday, their D800 worked perfectly in all flash modes, including Commander, when configured identically to my D800E.
I conclude that my D800E is not recognizing the Commander Mode, because:
1) The remote speedlights do not respond to the popup.
2) There is no "Fire Now" pulse emitted by the popup prior to shutter closing.
Next week the dealer is shipping it back to Nikon.
HBB in Phoenix, Arizona Nikonian Team Member
Photography is a journey with no conceivable destination.