Well then, your in luck. Cuz we have a lot of gameshark codes on this site!
http://www.supercheats.com/gameboyadvance/walkthroughs/pokemonsapphire-walkthrough03.txt
If that doesn't help, then you should just forget the Wailmers and use the codes to skip that and go directly to the elite four. Hey, glitches in games, they happen sometimes so if you don't want to use GS, I reccomend starting a new game.