This is a known bug. The bug is not on Spine's side.
Unity has this bug in 4.2 and fixed it in 4.2.1.

Unity 4.2.1 Release Notes wrote

Graphics: Fixed incorrect rendering order on meshes with multiple materials, introduced in Unity 4.2.

Download Unity 4.2.1 and you should be fine: http://unity3d.com/unity/download/

Apparently it isn't fixed in Unity 4.2.1. Below is the same exact scene using the exact same code. Notice the chin is drawn on top of the head, which is incorrect. Good job, Unity! :clap: Unity submeshes have been broken since July. :giggle: :puke:

Unity 4.1.5:

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Unity 4.2.1f:

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lol.
But SpineBoy was working fine for some reason, right?

Geez, I sure hope this gets fixed. I haven't actually used multiple atlases yet but we fully expect to, eventually.