Saving the modules page no longer (necessarily) rebuilds menus

Here's the code in system_modules_submit() - the function called when admin/modules is saved - that skips over flushing caches if no modules are enabled or disabled:

<?php
  // Gets module list after install process, flushes caches and displays a
  // message if there are changes.
  $post_install_list = module_list(TRUE);
  if ($pre_install_list != $post_install_list) {
    drupal_flush_all_caches();
    drupal_set_message(t('The configuration options have been saved.'));
  }
?>

So, drupal_flush_all_caches() is called only if something has changed, if a module has been enabled or disabled. (That function is what calls menu_rebuild() which is what rebuilds the menus.)