This definitely sounds fungal. The rust coloration is the give-away. The heat/moisture in his shoe from workout causes the flare-up.

There is NO over-the-counter medication that will kill nail fungus. I did read a medical report about a month ago, that a wierd home remedy might be effective. Involves washing/drying feet well, then massaging Vick's Vaporub into the toe/nail every night. No one has a clue why this works.