To the best Ive been able to figure out, TGA work only when ALL the textures being used are TGA. As soon as you throw a DDS file into the mix, thats when things start to go wonky.
Are *any* of the skins for the affected meshes using any .dds files at all? I think I remember reading a thread somewhere that suggested if the standard was using .dds, it would effect the rest of the skins this way.