That's a typo. The original spells had a breath weapon component and all had a casting time of 1 standard action and a duration of instantaneous (except animate breath, which had a duration iun rounds for obvious reasons). All the revised versions have a casting time of 1 swift action and a duration of 1 round, except for Stunning Breath. All the casting times were changed correctly but an unfortunate oversight left Stunning Breath at Instantaneous, which means:
The spell energy comes and goes the instant the spell is cast, though the consequences might be long-lasting.
Compared to Permanent:
The energy remains as long as the effect does. This means the spell is vulnerable to dispel magic.
So basically by RAW, your breath is stunning while the spell is being resolved, but loses that property once the spell effect has been resolved, since the spell energy is gone. And since the use of a breath weapon is no longer part of the same action as casting the spell, the Spell Compendium version does absolutely nothing
when cast by purest RAW.
But it's an obvious typo - given the way all the other instantaneous breath spells were revised the true duration is obviously supposed to be 1 round and would be house-ruled as such for the sake of consistency alone in any reasonable game.