Flash question

I have found the settings in the commander mode and was able to get my SB-900 to work with my D90 wirelessly. Even though I set the built in flash not to go off it goes off every single time. Can anyone tell me what I am missing?

The built in flash is firing as that's how it's communicating with the SB900. However in your setup, the on-board flash is not contributing to the lighting of your subject as it fires it's pre-flash signal to the SB900 before the shutter opens. So what you have is your on-board flash disabled but the commander mode is active through your built-in flash. You could also get the SU-800 as a dedicated flash commander instead of using the internal one.

It happens so fast I had no idea. Thank you.