Same issue for about a week for two of my toons. If you bring up Blizzard's quest tracker by bypassing Carbonite via Alt+L it's missing the quests as well.
While I don't have the time and patience to trace down the addon that's causing it, what has worked for me is a simple ui reload after I login. From then on my quests show, and new ones are processed correctly.
I will keep watching this thread in case someone happens to find out what's causing it.
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