I had the same problem as you and solved it with this. Use your first example, but your scripts() block should look like this:

    .scripts([
      paths.jquery + 'dist/jquery.js',
      paths.bootstrap + 'javascripts/bootstrap.js'
    ], 'public/js/vendor.js', './');

Note that I've reversed the last 2 arguments. This properly grabs jQuery and Bootstrap from the vendor/bower_components folder and concatenates them into public/js/vendor.js without needing to copy them into resources first.

sbarre is correct, they changed the order of the baseDir and outputDir here: https://github.com/laravel/elixir/commit/406bfcd2b8d05540c0b39...

It also messed up my scripts when I upgrades around that time.