So after going through both CSS files numerous times, turning things on and off, and troubleshooting. It turns out that the startbootstrap.com css needs all .navbar-collapse classes turned off, so comment out all the classes:
.navbar-collapse:before,
.navbar-collapse:after {
display: table;
content: " ";
}
.navbar-collapse:after {
clear: both;
}
.navbar-collapse:before,
.navbar-collapse:after {
display: table;
content: " ";
}
.navbar-collapse:after {
clear: both;
}
.navbar-collapse.in {
overflow-y: auto;
}