Permalinks Strip Category Not Working

I’ve been using your plugin since it was released and it’s been great! However, just today I noticed that the category was being stripped from my post url’s and when I tried toggling the permalink setting for that on and off nothing happened either way. My url’s are still not displaying the category url therefore getting they’re confused with some interior pages which is making a bit of a mess. The website is: http://bozartfamilydentistry.com Thanks for the help!

http://wordpress.org/extend/plugins/wordpress-seo/