I haven't been able to reproduce the blizz tracker reappearing yet. Once I do I'll see what I can do to fix it.
Try this. Create a new character, have everything loaded up for the UI. Go into the "Objectives" options and uncheck everything but "Instant Quest Text". In the QuestsFu options, check to "use Own tracker". Do the first few quests and you *should* have the problem occur. At least, that's what's happening to me. :) And thanks for the update!