Bodies can change alot in a short time in high school.
Look at the body types in your family, he may have put on muscle rapidly because thats what comes natural for him. I discovered that my running performance began to suffer when I was under 10 lbs. As for biking and swimming, I do not believe they harm running, but used intelligently can strenghten muscles which should be strenghtened to balance those used in running. The quads are a good example. The caveat here is overtraining, which should be considered as a possibility for explaining the decrease in performance.