Hi this is probably a bug in my .htaccess file because without the .htaccess in the root my jsecure works fine. All I need to do in the .htaccess file is redirect to my joomla directory. Here is the file:
-----------
RewriteEngine on
<IfModule mod_php5.c>
# mod_suPHP is active - php.ini overrides must be within these tags or in your local php.ini
</IfModule>
RewriteCond %{HTTP_HOST} ^site.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.site.com$
RewriteRule ^.*$ "http\:\/\/www\.site\.com\/home\/" [R=301,L]
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When I hit site.com/home/administrator/?secret with this .htaccess it redirects me to my index (even when i tell jsecure plugin to use custom 404).

Any advise about what I'm doing wrong would be greatly appreciated.

Regards,
Steve