They've got different roots. The bo's origins are Okinawan (ryukyu kobujutsu), the jo styles are Japanese and originated with Muso Gonnosuke. In other words, one is Japanese and one is not.
Mary, the bo is a prominent part of a number of purely Japanese traditions. Several schools of naginata have bo in their curriculum, as do other koryu, including Yagyu Shingan Ryu and Hontai Yoshin Ryu.
Gonnsuke was a practicioner of Tenshin Shoden Katori Shinto Ryu, and legend has it he fought Mushashi in a practice match using his bo, only to be defeated. After meditating on this in the mountains, he cut the bo down to the size of a jo and went back to have a rematch and to found Shinto Muso Ryu.
So, while the Okinawan systems definitly do have unique and distinctive bo work, the purely Japanese systems do as well.
--John A Butz