Have you accidentally knocked them out before? If so, rebattle the Elite 4 and they're be back.
When you arrive in the area, it should say something like "an electrifying presence is in the air".
If you have caught one of them, you cannot catch it again and nothing will happen when you enter during the time when it should appear.
Raikou appears in the first 20 minutes of the hour. Example: 3:10PM
Entai appears from 20-39 minutes. Example: 3:30PM
Suicune appears in the last 20 minutes. Example: 3:50PM
Once you catch one, you will have to leave the area before you can catch another.
If it still doesnt work, then either you are doing something else wrong, or your game has a problem. Also, Deoxys is not needed to find this trio.
