Pages Not Working With Custom Permalink

I’m trying to make it so the permalink for my pages and posts are “/%postname%/”, and I’ve tried it with the Post Name option as well, but every time I do it, it says “You should update your .htaccess now.” So I update my .htaccess file with what they ask me to put into it, but the links for the pages don’t work, and instead I get the error “The requested document was not found on this server.” If I change the permalink back to Default, the pages load fine. But, I want it to use the custom permalink, so what can I do to make it work?

Note: I’m using Bulletproof Security, and the .htaccess is located in /httpdocs/root/, as the root folder is where all the files for WordPress are in.