All the permalinks were working fine for me until I upgraded to WP 3.3 recently. My blog (example.com) is installed in /site directory (example.com/site) for WP.
Initially my permalink structure was /%category%/%postname%-%post_id%.html so an article would have complete url as example.com/gadgets/whis-and-that-2323.html but after upgrading to WordPress 3.3 a strange links started appearing. There was automatic insertion of the WP directory name in all my permalinks ie example.com/site/gadgets/whis-and-that-2323.html but the permalink settings and .htaccess file codes have not been changed.
How can I get rid of this WP directory automatic insertion in URLs? (PS: blog runs on top domain and WP installed in 'site' directory, website is configured well in index.php file)