For the short ribs: Place the olive oil, thyme, garlic and orange zest in a large resealable plastic bag. Add the short ribs and rub the marinade into the ribs. Refrigerate for at least 4 hours, or preferably overnight. Allow to come back up to room temperature before cooking.
Preheat the oven to 150 degrees C/300 degrees F. Heat a large Dutch oven over medium-high heat.
Wipe the marinade off the short ribs, reserving the marinade, and sprinkle generously with salt and pepper. Working in batches, brown the short ribs on all sides in the Dutch oven, 6 to 8 minutes per side. Remove to a plate.
Add the carrots, celery, onions and the reserved marinade to the pot and cook over high heat for 5 minutes.
Pour in the wine, bring to the boil, and cook for a few minutes, scraping the bottom of the pot with a wooden spoon.
Pour in the stock and then return the ribs to the pot, pushing them down to make sure they're submerged. Cover with a lid, transfer to the oven, and cook until the ribs are completely tender but still hold their shape, 2 to 3 hours.
Meanwhile, make the cheesy polenta: In a medium saucepan, bring the milk to the boil with 500 milliliters/17 ounces water and the bay leaf and thyme. Turn off the heat and leave to infuse for 20 minutes, then remove the herbs and bring back to the boil.
Add the polenta in a thin steady stream, whisking constantly. Cook for 1 minute (or according to packet instructions), until thickened, then remove from the heat and stir in the butter and Parmesan. Add salt and pepper to taste.
Finish the short ribs: When the short ribs are done cooking, transfer them with tongs to a dish and cover with plastic wrap.
Strain the braising liquid into a pan, discarding the vegetables, and spoon off excess fat. Whisk in the treacle, bring to a simmer, and cook over a low heat until reduced by half, skimming any fat and scum that rises to the top. Pour back over the ribs.
For the gremolata: Mix together the garlic, parsley, lemon zest and some salt and pepper in a small bowl.
To serve: Spoon the polenta into shallow bowls, arrange the short ribs on top, and spoon over some of the cooking juices. Scatter with the gremolata and serve.