In a medium saucepan, warm the broth over medium-high heat. Cut the vanilla bean in half lengthwise. Scrape out the seeds and add them, and the bean, to the broth. When the broth comes to a simmer reduce the heat to low. Add the butternut squash to the simmering broth and cook until tender, about 5 minutes. Using a slotted spoon remove the butternut squash to a side dish. Turn the heat on the broth down to very low and cover to keep warm.
Meanwhile, in a large, heavy saucepan, melt 2 tablespoons of the butter over medium heat. Add the onion and saute until tender but not brown, about 3 minutes. Add the rice and stir to coat with the butter. Add the wine and simmer until the wine has almost completely evaporated, about 3 minutes. Add 1/2 cup of the simmering broth and stir until almost completely absorbed, about 2 minutes. Continue cooking the rice, adding the broth 1/2 cup at a time, stirring constantly and allowing each addition to of the broth to absorb before adding the next, until the rice is tender but still firm to the bite and the mixture is creamy, about 20 minutes total. Discard the vanilla bean. Turn off the heat. Gently stir in the butternut squash, Parmesan, the remaining tablespoon of butter, and salt. Transfer the risotto to a serving bowl and sprinkle with chives. Serve