Features always exports the first vocabulary

  $objects = ctools_export_load_object('taxonomy_export', 'all', array($machine_name));
  $taxonomy_export = current($objects);

So it loads all taxonomies and selects the first. Correct behaviour would be to select only the taxonomy matching the $machine_name.

  $objects = ctools_export_load_object('taxonomy_export', 'names', array($machine_name));
  $taxonomy_export = current($objects);