Preheat the oven to 325°. In a large saucepan, melt the butter. Add the brown sugar and cook over moderately high heat, whisking constantly, until smooth and bubbling, about 5 minutes. Gradually whisk in the cream. Return the mixture to a boil, whisking constantly. Add the salt and vanilla seeds.
In a large heatproof bowl, whisk the egg yolks. Gradually whisk in the hot cream mixture. Strain the custard into eight 6-ounce ramekins. Set the ramekins in a small roasting pan and place it in the middle of the oven. Fill the roasting pan with enough boiling water to reach halfway up the sides of the ramekins. Cover with foil and bake for 1 hour, until the custards are set but still slightly wobbly in the center. Transfer the ramekins to a baking sheet and refrigerate until chilled, 4 hours.
In a medium saucepan, mix the sugar with 2 tablespoons of water and cook undisturbed over high heat, until a deep amber caramel forms, 6 minutes. Using a moistened pastry brush, wash down any crystals from the side of the saucepan from time to time. Remove from the heat. Add 2/3 cup of water and stir until smooth. Let the caramel sauce cool, then stir in the vanilla.
Top the pots de crème with the caramel sauce and whipped crème fraîche, sprinkle with Maldon sea salt and serve.