Are they the same quests as when you logged off? Most newer quests have them, but many of the multi-year older ones don't.
Also, make sure you don't have any POIs filtered (right click on the map, hit filter POI and make sure everything's checked). Lastly, make sure the quests are actually set to track in the quest helper (ie are checked in the journal window). Only the top ~10 (I think?) quests that are actually in the helper show the official ROIs/POIs.
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