Drush doesn't run drupal_flush_all_caches() after module enable/disable

Using 3.x with D7:

1. Enabling or disabling a module calls drush_module_enable() or drush_module_disable().
2. Those functions call the core module_enable() or module_disable() respectfully. Note that neither of those core functions actually call for a menu rebuild.
3. Drush then 'executes' the system_modules_form after the modules have been enabled. In http://api.drupal.org/api/function/system_modules_submit/7 the function drupal_flush_all_caches() is only called if any modules had their status' changed. In which case at this point using Drush is false.
4. Visit site with a new module enabled. Menu still hasn't been rebuilt and so you cannot view any of the module's pages yet.

We need to add a call to drupal_flush_all_caches() to drush_system_modules_form_submit() to emulate the proper behavior.