In a large saute pan, heat 1 tablespoon olive oil on high heat. Toss half the stew meat in 1 tablespoon flour and add to the pan. Brown the meat well, turning to get all sides. Transfer the meat to a crockpot. Repeat with the remaining beef, 1 tablespoon flour, and 1 tablespoon olive oil.
To the saute pan, carefully add the red wine (it will steam and boil!) Use a wooden spoon or spatula to scrape up all the browned yum-yums from the meat. Cook a minute or so until the wine is reduced to 1/2 to 2/3 c cups. Transfer this mixture to the crockpot.
Heat a new saute pan on high heat with 2 teaspoons olive oil. Add the onion cook until lightly browned. Transfer to the crockpot.
Heat the remaining 1 tablespoon olive oil in the pan used for the onions. Add the mushrooms and cook, stirring occasionally, until mushrooms are browned. Transfer to the crockpot.
To the crockpot, add the beef broth, pepper, and thyme sprig. Cook on low 6-7 hours or until meat is very tender.
In a small bowl, use a fork to mash together the remaining 2 tablespoons flour and the butter to make a beurre marnier. Stir into the crockpot (this will thicken and flavor the gravy). Let cook another 30-60 minutes and serve. Season to taste (mine needed 1/2 t kosher salt) and add the remaining 2 teaspoons fresh thyme leaves. Serve over mashed potatoes or buttered egg noodles.