Dredge the beef cubes in flour seasoned with salt and pepper. Heat a heavy Dutch oven over medium high heat, add a drizzle of oil, and brown beef in batches, refreshing oil as needed – take care not to burn the pan. Remove browned meat and reserve. Meanwhile, blanch butternut squash in salted water for 2 minutes – reserve.
Refresh pan with oil if needed, add onions and sauté until tender, scraping pan regularly with a wooden spoon to break down crust. Add Marsala and stir to finish deglazing, reduce by 25%.
Add browned beef, stock, and blanched butternut squash. Bring to a boil, skim, reduce to a simmer, cover and simmer until the meat is as tender as you like (about 1.5 – 2.5 hours on the stove or in a 300 degree oven).
Serve over Creamy Grana Padana Polenta, egg pappardelle, mashed potatoes or wild and brown rice.