I'm having the same issue with my Bounty Hunter. My log-in screen says I've finished the story with my BH. I've received the <Reckoning> Achievement via completing the Bounty Hunter missions on Corellia. I've even unlocked the Heroic Moment Ability (Flamethrower) via completing chapter 3. But I haven't received credit for <Chapter 3: Bounty Hunter> nor have I received my circular signs.

My bounty hunter is also having the same issue. D: