Oh! I just re-read that. Hmm..did you beat the other 6 Gym leaders Brock, Misty, Lt. Surge, Erika, Sabrina, and Koga? You have to make sure you also beat the Rocket Hideout in Celadon's game corner, and chased them from the Siph Co. Building in Saffron City. Giovanni then returns to his gym after you beat Blaine. If you did all that then it sounds like a fluke..hmm..