But isn't it weird that all other stats are what they should be? I've only got 5 badges at that point, so it seems quite exceptional that every stat is boosted except Sp.Atk.
If he has 30 Sp.Atk EV's, his stat is 94
If he has 100 Sp.Atk EV's, his stat is still 94.
Nonetheless, with 100 Sp.Atk EV's he deals significantly more damage than when he has 30 Sp.Atk EV's.
Edit: After beating the sixth gym, his Sp.Atk stat went immediately to 110, so everything is fine now, I guess.