Cook the kielbasa in the olive oil in a large heavy soup pot over high heat until golden brown, 5 to 6 minutes. Add the onions, salt, black pepper, and bay leaves and cook, stirring, until the onions are slightly caramelized, 12 to 15 minutes. Add the garlic and cook, stirring, until fragrant, about 1 minute. Sprinkle the flour over the onions and cook, stirring constantly, for 2 minutes. Gradually whisk in the stock and the beer. Add the thyme and bring to a boil. Reduce the heat to medium-low and simmer uncovered, stirring occasionally, for 1 hour.
Add the cheese, a little at a time, stirring until nearly melted after each addition. Remove from the heat, taste, and adjust seasoning if necessary.
Ladle the soup into bowls and garnish with the Cheesy Popcorn and minced fresh chives.
Makes 2 quarts, 8 servings