Madelyne might have been more than a clone of Jean Grey but she was not a Phoenix fragment. Madelyne was living but inert until Phoenix/Jean Grey sacrificed herself on the moon and Jean's tainted life force was sent back to her with the intention of reviving her as she laid at the bottom of Jamaica Bay -- Jean Rejected the Phoenix Fragment and the memories that came with it and both went to directly to Madelyne bring her consciousness instead.