I am having the same issue and opened a bug report ticket for it.
I also experienced this same exact thing on my Hunter. I simply just wanted to get to Maldraxxus (for the undead pet tame thing). Did Intro, and then couldnât take the portal up the Flight Master and wasnât prompted to start Threads of Fate or the Campaign.
-That being said, if not interested in the Campaign at the moment until they fix it, you can take the Dornogal Timeways Portal into Ardenweald that you use to get to Mists Dungeon for S1. From there you can take a Flight Point to where ever (if you have them unlocked? I suppose) and I was able to enter Plaguefall Dungeon. Unsure about Raids but I imagine it would be possible.
Yep having the same issues here hoping they get it fixed sometime soon 
its kinda crazy an entire xpac is broken for some characters, blizz has a fix, but theyre waiting until mid dec to launch it. like this is what hotfixes are for
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