I suggest changing core/Tracker/Visit.php from:

/**
 * Returns true if the last action was done during the last 30 minutes
 * @return bool
 */
protected function isLastActionInTheSameVisit()
{
       return isset($this->visitorInfo['visit_last_action_time'])
                               && ($this->visitorInfo['visit_last_action_time']
                                       > ($this->getCurrentTimestamp() -
Piwik_Tracker_Config::getInstance()->Tracker['visit_standard_length']));
}

/**
 * Returns true if the last action belongs to the last Visit.
 * This is usually true, when the previous action was done during the last 30 minutes.
 * Provides hook for individual splitting of visits.
 * @return bool
 */
protected function isLastActionInTheSameVisit()
{
       $belongsToLastVisit = isset($this->visitorInfo['visit_last_action_time'])
                       && ($this->visitorInfo['visit_last_action_time']
                       > ($this->getCurrentTimestamp() - Piwik_Tracker_Config::getInstance()->Tracker['visit_standard_length']));
       Piwik_PostEvent('Tracker.isLastActionInTheSameVisit', $belongsToLastVisit,
                       array('visitorInfo' => $this->visitorInfo, 'request' => $this->request, 'idsite' => $this->idsite));
       return $belongsToLastVisit;
}

public function isLastActionInTheSameVisit($notification)
{
       $belongsToLastVisit = &$notification->getNotificationObject();
       $info = $notification->getNotificationInfo();
       $referrer = new Piwik_Tracker_Visit_Referer();
       $refererUrl = Piwik_Common::getRequestVar('urlref', '', 'string',
$info['request']);
       $currentUrl = Piwik_Common::getRequestVar('url', '', 'string',
$info['request']);
       $refererInfo = $referrer->getRefererInformation($refererUrl,
$currentUrl, $info['idsite']);
       if(in_array($refererInfo['referer_type'], array(2,6))) # Ignores
direct entries.
       {
               $belongsToLastVisit = false;
       }
}