In a large pot over medium heat, melt butter and saute shallots for 3 minutes.
Add corn, potatoes, stock, thyme, vinegar, and salt. Bring to a simmer over medium heat and then reduce the heat to medium-low. Cover and simmer for 20 minutes or until the potatoes are fork-tender.
In a bowl, whisk together the milk and flour.
Remove soup from heat and whisk in milk mixture. Return to heat, raise the heat to high, whisk, and cook for about 3-5 minutes or until thickened.