public function onAfterInitialise()

	{

		$params = JComponentHelper::getParams('com_cmandrill');

		$appl = JFactory::getApplication();



		$this->loadLanguage('plg_system_mandrill.sys');



		$key = $params->get('apiKey');



		if (strlen($key)) {



			$path = JPATH_ROOT . '/plugins/system/mandrill/mailer/mail.php';



			JLoader::register('JMail', $path);

			JLoader::load('JMail');



		} else {

			$appl->enqueueMessage(JText::sprintf('PLG_SYSTEM_MANDRILL_NO_API_KEY_SPECIFIED', JRoute::_('index.php?option=com_cmandrill')), 'warning');

			return false;

		}

	}

If the plugin is enabled we don't use the SMTP configuration, but the mandrill API.

Do you use:

$mail = JFactory::getMailer();

$mail->send(....);

or how do you exactly send your mails?

Also try to have the plugin ordered first in the plugin list (first for system tasks).

That is what pops up into my head right now.

Regards,
Daniel

$mail = JFactory::getMailer();

$mail->send(....);

$mail = JFactory::getMailer();

$mail->send(....);