Right now we do drupal_flush_all_caches() at the end of the import process. This guarantees that things like menu system additions get picked up (we ran into this problem while testing importing views.) However I am worried this is a little too big of a hammer for all situations. For instance, this would clear the page cache which we would really only need on field system changes. We should look into what caches we realistically should be clearing on every import, and then implement other clears as needed in the module-specific import handling.