Hi,
Since both W3 and the All-In One security use Rewrite rules to work the order of plugin activation may change how htaccess is setup and works. Try turning on the security plugin before you tune W3, and also try vise versa - enable W3 and then security. I know with Ithemes Security it automatically preserves htaccess and always puts it settings at the top of htaccess so that plugin enable order effects are minimized. Review your htaccess files on the working sites and compare them with the non working site and I will bet they are different or have a different order...
