I recently discovered that when my SB-900 flash gun is taken off camera, the flash is weaker than when it is mounted on the hotshoe. At the camera club tonight, I discussed this with a couple of Nikon owners and I found something very interesting. Now I understand that the SB-900 is not fully communicating with my D90. The SB-900 and the D90 will both show TTL option, but unlike the higher end Nikon DSLR's, they will not show the Remote option. The Remote option is what communicates the Aperture and Shutter speed settings to SB-900, but not the TTL option.
In short, the D90 is not fully communicating with the SB-900 although it has the built-in Commander mode to control the flash wirelessly. Knowing this, the best option may be to use the Commander in manual mode (not TTL) when using the flash off-camera.