Has it always had a stock filter? Generally running an aftermarket stock replacement (K&N, etc) doesnt require jetting nor will it have any adverse effects if everything is right to begin with. If the bike had pods on it (and subsequent rejetting) and then you went back to stock airbox/filter, then its a possibility. Other than that I cant think of any way the air filter would cause a rich mixture, unless its REALLY dirty. Id say you probably have a fuel problem. Have you done any carb work or intake/exhaust mods? Rejetting, rebuilding, etc etc?