Using WordPress’s permalink feature seems to cause some issues with password protected directories that use Apache’s .htaccess to handle authentication. I recently had to troubleshoot why after installing WordPress on the root level of the domain that a password protected directory would return a 404 page instead of the typical login box.
The problem comes from the Apache rewrite engine that WordPress uses to make search engine friendly URL’s. WordPress uses a .htaccess file in the root folder of the install to take any URL and allow WordPress to process and serve the appropriate page, or error.
