No rewards for killing story mode boss.

I killed the Tracker boss in the Toxic Fume March, but during the middle of the fight i got revenged. The confirmation button to replay or exit the fight screen did not appear as per half the time i engage in any revenge or carribean pvp since the update so i had to refresh. I came back to find i beat the boss a but i got no initial rewards from completing the area, the shuffle, nor the +1 to command, strength, or intelligence. Can anything be done about this or am i screwed for that area?