Cita: register_long_arrays boolean
Tells PHP whether or not to register the deprecated long $HTTP_*_VARS type predefined variables. When On (default), long predefined PHP variables like $HTTP_GET_VARS will be defined. If you're not using them, it's recommended to turn them off, for performance reasons. Instead, use the superglobal arrays, like $_GET.
This directive became available in PHP 5.0.0.
Por lo que deberias checar que esta directiva tenga asignado false.