Crud, I'm playing the level with the psycho hunter guy and when I enter the hanger with my ship another Jaden shows up and nothing else happens. I could start over, but I'd hate to have the same problem again and I also tried checkpoints, but that didn't help either. Is there maybe something I could try in the console load up the battle maybe?

Just went ahead and played the level over without saving until the boss fight, must have been something nasty hiding up in the save data or something. :)