In a large stock pot, melt the butter on medium heat.Add the sliced onions and bay leaves and sauté until the onions are golden brown.Add the thyme and flour and continue to sauté for 3 minutes.Add the balsamic vinegar and wine and cook for 2 more minutes or until the wine evaporates.Add the broth and black pepper and continue to cook for 15 minutes.Portion the soup into 6 oven proof bowl.Place two slices of the toasted baguette on top, cover with gruyere and parmesan cheese.Broil in the oven until the cheese bubbles and turns golden brown.