In 6-quart stockpot, melt butter over medium-high heat. Stir in onions, thyme, salt and pepper. Cook about 15 minutes, stirring frequently, until onions begin to soften and turn golden. Stir in vinegar and molasses. Cover; reduce heat to medium-low. Cook about 20 minutes longer, stirring occasionally, until onions are softened. Remove from heat; cool slightly.