EDIT: This solution is not viable for newer versions of Bootstrap, where the navbar-inverse and navbar-static-top classes are not available.
Using MVC 5, the way I fixed mine, was to simply add my own Site.css, loaded after the others, with the following line:
body{padding: 0}
and I changed the code in the beginning of _Layout.cshtml, to be:
<body>
<div class="navbar navbar-inverse navbar-static-top">
<div class="container">
@if (User.Identity.IsAuthenticated) {
<div class="top-navbar">