Happened to me as well. What happens is the dealer has a production slot which is available and they order a car for general inventory. That is what shows initially in the system when you look online. After a few days the system will update.
When I ordered my M3 it was originally a 335 my dealer was ordering for their inventory. They gave me that production slot and changed the order to my specs. My first look online showed the 335 as my dealer had ordered it.
I say don't worry, even when the system updates it may not show all your options. To be sure, get a copy of your order from the dealer listing all options...
2011 Space Grey E90 M3, DCT, Comp. Pkg.
1997 Z3 2.8, Artic Silver, Tanin Red interior, MT
1974 2002tii, Inka, MT