[Maeby]

I'm not sure if this information is of any use, but the quests that aren't showing seem to be breadcrumb quests that lead either to a different zone, or a different area within the zone. Once you get to a hub, it seems that all the "Go kill 12 of these" type of quests are tracking fine. The ones that are missing are the ones that are more like "Go speak with Some Panda-guy in the Area of More Quests".

Maybe Blizzard reports quests like that in a different way, and Carbonite isn't picking those up? Since I have no idea what I'm talking about, I'll let you figure that out. =]