Well, something is messing with your default tracker then, because, as you said, it's only displaying two quests.
The tracker has a default height of 140. However, it actually is rendered larger because its height on screen is determined by two anchor points. One for its top-right and one for its bottom-right. If ClearAllPoints() is called on the tracker, and only one anchor point reapplied (as all the scripts and addons I've seen floating around here will do, as well as something like MoveAnything), then the tracker is set to its default height of 140 (only large enough for 2 +/- quests).