Exodus (2) - S2-E23
Trivia: Throughout this episode, the Superman theme tune can be heard at various points being played very softly and slowly. The first time it is heard, it is only the first few opening keys, but the last time it is heard, it is fully played.
Answer: The kryptonite only creates mutations when it reacts with the environment and an individual. Remember, the FDA and several environmental groups did check out Smallville after the meteor shower, but found no danger in the rocks. Obviously they're not always emitting mutating rays, or all the flora and fauna of the surrounding area would be horribly mutated.
Phoenix