What does the description of the Agile Breastplate say ?
Benefit: The armor check penalty for Climb checks and jump checks is only –1 (masterwork and mithral versions of this armor reduce this penalty as well as the normal penalty).
Nothing about the fly skill, or dex based skills in general, so it does exactly what it says it does, nothing more.
I'm assuming you're the GM. Maybe charge a little extra, or make 'em find a particular armor smith that specializes in armors for flying creatures.