YupDid you set them as read only?
I mean... that when ever i install a Custom skin for my Weapons only the GL wears the skin and the rest are still the same, It might do with the fact that im using legions lite? I'm not sure =/dude....make backup copies of the files that you've got no problems with and then just go to the live folder and click on properties then deselect Read only..and then update the Game!!