Twilight Princess GameCube control issues

The GameCube Twilight Princess ROM works great, but the moment I get to the part where you need the right z button in order to progress, (use Midna to jump across ledges) the button doesn't register. When I test it in the config menu it works, but it doesn't regester in-game.
I've tried looking into finding a Wii ROM instead, but no luck... Any ideas on how to fix this problem or find a different option? Thx!