I think it depends on when you're trying to skin him (in the campaign or in a Skirmish). I've not investigated, but from what I've heard the new wargear (or the wargear menu at the very least) mean that the FC isn't colourable like normal.
What it could be (especially with the uber-gold levels of the new FC) is that the majority of the old skin is overriden by the new additional texture that handles the wargear, and it's just that the wargear is over almost all of the old texture.
He's certainly skinnable, though, as
Rhedd has released a few skins for him (replacing the baby face in some of them)
As for the separate issue of distorted badges, it sounds like your badge is suffering from wrapping issues. Because the Marine's shoulder pad is round but the texture is flat then some areas of it have to wrap in strange ways. If you look carefully then a lot of badges that should be perfectly round or straight in some areas aren't because of the curve of the shoulder pad. The only solution is to us a smaller badge that is just a shape rather than some block of image that has to be perfectly shaped to look right.
[edit] Moving to DoW Skinning