I've recently updated core from 7.9 to 7.17. Things seem to be working correctly, except, all system generated links are no longer recognizing the correct base path. I have my install in a subdirectory so the base path is mydomain/subdirectory. No problems in 7.9, but now all system generated (including menu) links only render the top level/root (thus excluding 'subdirectory') as the base url. The htaccess file is working correctly (as is clean url's). And drupal is rendering the correct base_url when I test print the $base_url. Any ideas?