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/406bfcd2b8d05540c0b39e897291c2b97019a7d6
It also messed up my scripts when I upgrades around that time.
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