Commander Kiva is with the Lucian Alliance. She is aware of the Destiny and has a list of all the people who are aboard it. She is also aware of the long range communications devices that the crew of the Destiny have been using to keep in touch with the people back on Earth.
The implication is that there is someone who is involved with the Stargate Program, and the Destiny in particular, who has been spying on the Lucian Alliance's behalf. In the hope of finding Destiny after got attempt of the co-ordinates Destiny travels through she revisit these planets in the hope of catching up with the ship and sieze control