So you're using it in a plugin? Most plugins make a call to AppController::setPagination($get, $settings, $ajax) to load and set the pagination from the config. The Blesta.pagination_ajax value in the config is used when the third argument, $ajax, is true. This value does not get overridden.
If you want to override the AJAX pagination behavior, don't call AppController::setPagination. Instead, load and set the pagination yourself.
// Load pagination
$this->Pagination = $this->getFromContainer('pagination');
// Set GET params
$this->Pagination->setGet($this->get);
// Your pagination settings merged with your custom pagination settings
$this->Pagination->setSettings(Configure::get('Blesta.pagination'));
// Make Pagination available to the view
$this->view->Pagination = $this->Pagination;