Actually, the game is supposed to work that way.
When you earn a Pokeathlon medal for a specific Pokemon, it is just accounting the fact that you used a pikachu to earn the medal, but it doesn't take into account that a specific Pikachu won a medal.
This is especially proven by the fact that the second room only counts how many medals you have earned with a certain species of Pokemon.
Excerpt from Bulbapedia:
By winning events in the Pokéathlon, the participating Pokémon will earn medals for their species.