Hi,
I'm quite new to the SB900 so I don't think I"m going to be a great deal of help, I'm sure someone more knowledgeable will come along soon.
Just a few thoughts, have you got your SB900 set to remote, and your D300 set up so your built in flash is in commander mode?
Also, have you got the same channel and group selected on the SB900 and in the menu of your D300?
Other than that I can't think of what might be wrong, I'm able to control flash output of my SB900 from my D700 remotely without problem,
Julie