Season the beef cubes with the salt and pepper and dredge with the flour. Shake off any excess.
Melt 2 tablespoons of the butter in a large heavy skillet over high heat until hot but not smoking. Add the beef cubes and sauté until nicely browned on all sides. Work in batches so as not to crowed the beef cubes, or they will steam instead of sauté. Add 1 tablespoon of butter, if necessary. Transfer the beef cubes to a heavy Dutch oven.
Add the remaining 1 tablespoon of butter to the skillet and melt over medium heat. Add the onions and cook, stirring occasionally, until browned, about 15 minutes. If necessary, raise the heat toward the end of the cooking time. It is important to brown the meat and onions evenly to give the stew its deep brown color. The trick is to stir the onions just enough to avoid burning them but not so often as to interrupt the browning process. Combine the onions with the meat in the Dutch oven.
Deglaze the skillet with the beer, scraping with a wooden spoon to loosen any brown bits, and bring to a boil. Pour the beer over the meat. Add the thyme and bay leaves.
Simmer, covered, over low heat until the meat is very tender, 1-1/2 to 2 hours. Before serving, stir in the red currant jelly and vinegar; simmer for 5 minutes. This sweet-and-sour combination will give this hearty stew its authentic Flemish flavor. Remove the thyme sprigs and bay leaves. Taste and adjust the seasoning and serve.