I just started playing with the Character Animation tutorial, and I'm a noob at animation, so take this for what it's worth. :) But what I suspect is happening is this:

Regarding how Animations work - they are a set of Keys (IPOs) for a set of Bones, where those Bones alter the Mesh (I'm sure it's more complex than that). However, when you are making an Animation, you have to pick which Bones are Keyed, and move them. The 3D package won't create a Key for every single Bone in the model. So if you do not Key the particular Bone for a particular section of the Mesh, it won't be changed.

The Jump Animation may have just not Keyed a Bone in the model's neck. It's hard to tell from running it, but it looks like just the spine is moving in the upper area. If so, then running Jump wouldn't change the neck Bone's setting - it would stay whatever it was before. Which could be either rotated from Idle, or neutral.

So the Jump Animation is over-riding the Idle animation, there is no mixing. But it's only applying it's own Keys, which may not include the neck or head.