If you run the TextureEnder.jar (Convertor from Texturepack -> Resourcepack) The cobblestone gets the StoneBrick texture.
This is not a bug in the texturepack I used. This is since I converted it.
Environment
TextureEnder.jar: http://s3.amazonaws.com/Minecraft.Download/utilities/TextureEnder.jar
This happens to me, too. If you wan't to switch it manually, then you need to make the cobblestone texture be called "cobblestone" opposed to stonebrick. Then, you need to make the stone bricks texture be called "stonebricks".