Bootstrap uses offset to resolve spying only, not scrolling. This means that scrolling to the proper place is up to you.
Try this, it works for me: add an event handler for the navigation clicks.
var offset = 80;
$('.navbar li a').click(function(event) {
event.preventDefault();
$($(this).attr('href'))[0].scrollIntoView();
scrollBy(0, -offset);
});
I found it here: https://github.com/twitter/bootstrap/issues/3316