www.mysite.com <-- this to access CodeIgniterCMS based website
www.mysite.com/phpMyAdmin <-- this to access phpmyadmin installation, which currently inaccessible and just showing CI's default 404 error page
What should you do to able to access phpMyAdmin?
Answer is pretty simple. Your htaccess is not poking a hole through to let access to phpMyAdmin. Fix the htaccess like below
RewriteEngine on RewriteCond $1 !^(phpMyAdmin|index\.php|robots\.txt) RewriteRule ^(.*)$ index.php?/$1 [L]
Then you are good to go.