right... could you give me a hint as to where to start looking? What about the skin or the model would cause these differences?

.. With the eye poking through the eyelid I would guess that the eyelid's skin is just too close to the eye, and the z order gets reversed, maybe due to some rounding thing the engine does. That's easily testable and fixable. But I'm really pretty stumped as to what about my model could be causing the other things I'm seeing.

Like, what would cause the lower edge of the eyelid to appear much lower in the game than in MED:



As you can see, in the game the eyelid actually cuts into the cheek, while in MED it isn't even closing the eye fully. This is the same frame of the animation we are looking at.