At 3pm, Jack pulls his chains out of the wall, but they are still attached to his arms. When he runs into the soldiers and puts his hands up, the chains have disappeared.
Near the end, the Doctor says time has been reversed to a point after the President had been killed, but before the Toclafane appeared. However, in "The Sound of Drums," the President was not killed until AFTER the Toclafane appeared. (President Winters was killed BY the Toclafane, on the orders of the Master.)