Hey there! I have a facial rig that's based on the Gears of War 3 one (http://www.unrealengine.com/files/downloads/Jeremy_Ernst_FastAndEfficietFacialRigging2.pdf) So, it's a head that's skinned to a bunch of helpers. Those helpers are children of an offset controller (to fix bad poses etc). And those controllers are…
The bones (helpers) you want to export need to be constrained not parented to the offset controllers. Page 15 of the PDF you linked to. Maybe you can post a screenshot of the hierarchy in the schematic view so we can get a better idea on how you set up your scene.