Yeah, it counts all the zombies you've killed since you first played the game. I played a lot of Mercenaries: UC, Catacombs, and MtD stages. I'm not too fond of the J'avo maps.
They didn't do that for J'avo Massacre so I doubt they're doing it for this, are you sure it's not a glitched score? I've well over 10k kills but my score at the moment is only 417. If they counted all the zombies killed since people started playing the game I'd say the target would've been met 10 times over by day one!