if you let the camera choose the focus point, it will choose use the one with the closest subject. on a face it will focus the nose not the eye.+1, looking at those images given the position of the focus points I'd say that's the case. 5D3 allows the focus point to be easily be moved with the joystick so the total auto-selection modes are an abomination in my opinion.
i shoot portraits with one point focus and ai servo, if i dont have to recompose. maybe it helps to only let the camera choose cross-type points.