I'm fairly sure the You Are Not Alone was purely about The Master - I'm sure it would have mentioned in the trailer if Captain Jack turned up in the next episode, after all.
Anyway, I was thinking that "daughter" in this might not be meant in the conventional sense - did anyone else notice how the camera kept swinging back to his hand-in-a-jar while the Tardis was going haywire? I reckon she has the Doctor's DNA from the hand (which, after all, could have been anywhere before Jack found it or when the Master had it), and hence be a sort of daughter...
In fact, if this is true, and the DNA was taken by the Master, then it would make sense for her to be the woman with the red fingernails
