I have WordPress installed in a subfolder called news, but links to comments, posts, categories, etc all link to domain.com/?p=99 instead of domain.com/news/?p=99. The only link that points to the correct folder is the edit post link.
I have set my WP folder to, domain.com/news, and my site domain, domain.com. I also tried deleting my .htaccess file. Nothing has helped!
Part of the issue might step from the fact that WP used to be installed in the root folder.
Any idea what I can do? :(

newssubfolder? – Andrei May 30 '12 at 12:07index.phpto the root folder. I don't want the www.domain.com/ to be the WordPress blog. Only www.domain.com/news/ – Django Reinhardt May 30 '12 at 19:27