I assume questie hooks up the Questtracker somehow.
Questie notices if you track a quest, but doesn't notice if you track an "area" in EQL.
If I run into this issue, I always tick all Quests until the questie tracker doesn't show anything,
then I click on every "area" in EQL until all checkmarks are gone to start from clean.
Questie will then follow every quest you explicitly tick in your EQL3.
Then you should avoid tracking quests per area and instead only track explicit quests.
You might want to ask in the Questie Thread aswell,
because as long as Questie is used, their Questtracker will be used.
Sorry for the bad news
