There's more than one Barret model; he has four for each type of weapon (he has four attack animations; melee, gun, cannon, and Microlaser). You'll need to apply a custom model to all four. What's likely happened is you've changed the first one (melee) but in-game he starts out with a ranged weapon which is his second form.
It should SBAA, SCAA, SDAA, and SEAA; that's from memory though, so check 'em before changing them!