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I've had this problem a couple of times, even had the standard blizz tracker show up and the carb quest tracker load minimized. So far for me clicking the little minimize button a few times has generally resolved it. Seems to only happen at login and after a reload. I would look somewhere in the minimize function for the quest tracker I think, because after I get it to open up and the blizz tracker goes away it takes several clicks to get the carb version to minimize again.
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