Oh, and here's a little something from the Beast Wars Sourcebook in regards to Optimus Primal:

Originally just one of dozens of starship captains in the Maximal fleet, Optimus Primal's true calling was destined to be far more significant than merely trawling deep space exploration lanes. ... Thrust into the role of a military leader, he proved time and time again that he was an effective warrior who also possessed great compassion, loyalty, honor and even a wry sense of humor.
- page 3, BW Sourcebook 3.

So there you have it: In the CGI show, Primal was just an exploration ship Captain and NOT the Matrix-wielding, Convoy Council sitting, Cybertronian hero that the Japanese movie portrayed him to be. Whoever the Optimus Primal was in the Japanese movie, he is a different Optimus Primal from a separate continuity. The Japanese creators may have set out to try and link it to the CGi show, but they didn't, they created their own continuity.