We see this every year. The restaurants that are left off the current 2009 list are not owned by Disney. It takes longer for the dining plan participation contracts to be finalized for non-Disney restaurants. By the end of the year most, if not all, of these restaurants will be returned to the list.
Last year the major holdout was Teppan Edo, it took them forever to finalize their contract and be added to the dining plan list.
There are already threads on this topic and I am merging them into this thread.