Tuan,
If you are still seeing the SSID in beacons, it's not coming from any APs that are managed by this controller...unless maybe the APs were already configured to broadcast the SSID and then the controller was upgraded but the APs were not.
Question: How are you confirming that the SSID is still being broadcast?
I suspect that you are seeing the SSID coming from some other APs.
The only way to confirm is to locate the BSSID of one of these broadcast and then determine that the BSSID is coming from one of your APs.