Hmmmm....... I took a look Ross, but your skin uses lots of those nested layers, and I never really understood all that! LOL. However, I can see that many of your layers still have "FX" next to them, meaning the layer style is still editable, and in my experience Xion will not display layers properly if the style is still editable.
If this is the case, then you have a very long day ahead of you flattening all those layer styles, and the only way I know to do that is to create a new blank layer above the one you need to flatten, and then merge those two layers together. Unfortunately, this takes away the layer name and you have to type it out again!! Total pain in the ass, right?
I could be wrong Ross, so please ask someone else before you go ahead and edit the layers further.
Sorry I can't help any further...... I haven't skinned for a long time now, and most of the stuff has gone from my old brain!