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.
Heat oven to 350°F. Grease 8-inch round cake pan with shortening or cooking spray. Divide dough into 4 equal portions. For each portion, on lightly floured surface, roll into 5X7-inch rectangle. Place 1 slice Swiss cheese on each rectangle. Top with caramelized onions, divided evenly between rectangles. Place 1 slice Swiss cheese on top of onions. Starting with shorter side, roll up tightly. Press edge of dough into the roll to seal edge.
Using a sharp serrated knife, cut each roll into 2 (2 1/2-inch) slices. Place slices in pan, gently pressing down until slices touch each other. Bake 35 minutes or until golden and cheese is bubbly. Cool 5 minutes before serving.