I've noticed something similar on Artisan of Arms: Guardian's Pistol; though the achievement does occasionally progress for me, it is far from every kill. I suspect the issue has to do with not counting the kill if the final blow is dealt by condition damage. That's kind of a big problem, since every guardian pistol skill applies a damaging condition.
I don't know if this could be related to your situation, though. Were kills being counted consistently before you hit 103?