Is YouTube themselves working with to clear this music? Is it marked in YouTube's ContentID system somehow? Some artists have had copyright strikes placed against THEM for one of their original songs because someone else used their song (with permission) and then had YT's ContentID mark the other publisher as the owner.
It has got to be a slap in the face to generously offer your art for this use, only to be punished for doing so. Especially with the only way to deal with it is with a tone-deaf automated system.