Steps to reproduce the issue

For reproducing this bug yuo should use drag and drop option for reordering objects in the list. If object has any permission options set, once you change the order of that object in the list, JModel->storeorder() method (JTable defined function I suppose) is reseting permissions to defaults.

Expected result

Permissions untouched and order applied.

Actual result

Order applied but permissions reset to default.

System information

Joomla 3.4.1

Additional comments

In most cases I saw the usage like this:

    public function saveOrderAjax()
    {
        $pks = $this->input->post->get('cid', array(), 'array');
        $order = $this->input->post->get('order', array(), 'array');

        // Sanitize the input.
        JArrayHelper::toInteger($pks);
        JArrayHelper::toInteger($order);

        // Get the model.
        $model = $this->getModel();

        // Save the ordering.
        $return = $model->saveorder($pks, $order);

        if ($return)
        {
            echo "1";
        }

        // Close the application.
        JFactory::getApplication()->close();
    }

I think it should be changed in favor of using JSON result here like this:

    public function saveOrderAjax()
    {
        $pks = $this->input->post->get('cid', array(), 'array');
        $order = $this->input->post->get('order', array(), 'array');

        // Sanitize the input.
        JArrayHelper::toInteger($pks);
        JArrayHelper::toInteger($order);

        // Get the model.
        $model = $this->getModel();

        // Save the ordering.
        echo json_encode($model->saveorder($pks, $order));

        // Close the application.
        JFactory::getApplication()->close();
    }