Remember, Kloxo-MR only using for /etc/php.ini for execute php. When I try your php.ini in my test vps, I didn't error.
Just copy your php.ini to /etc/php.ini and then running 'sh /script/restart-web'. After that, testing all webmails (roundcube and others). all applications running well.
My system using nginx-proxy and php53u.
So?.