I shot a few photos with my D800E set in commander mode, using an SB800 and it worked without a problem. Do you have any falsh exposure compensation...or exposure compensation...set? Is your SB900 set in Remote mode with the correct channel and group? Is the "eye" (I can't remember the correct name right now) of the SB900 turned toward the camera so it can see the signal from the commander flash? Status of batteries in the SB900? That's all I can think of at the moment. It should work.