Check the abandon missions terminal at the tower. On my main character It had the Croda and Wolves story lines as abandoned, even though I had finished them before the expansion. Don't know why. If you're seeing the same thing then that might be what's causing the problem
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Kiosks are empty. When ttk dropped all year 1 missions were converted to quest form and put there. Most accounts of this issue however have players with an empty quest kiosk and all DB quest competed. Thanks for the suggestion though. :)