Superman doesn't detect kryptonite. He is just affected by it's radiation. However the effects of kyrptonite on Superman are never consistent or even proportional in any of the comics, shows or movies. Even within the same comic or movie it seems to be up to the writer at that moment to determine the effect that kryptonite has on Superman. For instance in the movie Superman returns he is affected by a small piece and is basically powerless however later he is able to lift a large island of it and fly it into space.
So for the specific instance you mentioned I would assume that the bullet was deemed small enough and the metal of the gun enough of a dampener for the radiation that the writer didn't have Superman immediately double over as if he had an irritable bowel.