i have the same problem, but with some of the skins,
for instance , if you choose the "windows aero" skin firefox is skinned correctly, using its own skin engine
but if you choose other skin, the skin overwrites firefox's skin
so you have to choose windows aero skin, then apply the changes, close firefox , open firefox
then apply any other skin, and again close firefox , open firefox, it should work
but the minimize, restore and close buttons are still skinned, even if firefox is in the exclusion list
so basically i need firefox won't be skinned by any skin, because it has its own skin engine