Alerts page mark read/viewed alerted inconsistent with alerts pop-up

The alerts page call flow is;
PHP:

        $alertRepo->addContentToAlerts($alerts);
        $alerts = $alerts->filterViewable();

        $skipMarkRead = $this->filter('skip_mark_read', 'bool');
        if ($page == 1 && $visitor->alerts_unviewed && !$skipMarkRead)
        {
            $alertRepo->autoMarkUserAlertsRead($alerts, $visitor);
            $alertRepo->markUserAlertsViewed($visitor);

            $this->markInaccessibleAlertsReadIfNeeded($alerts);
        }

But alerts pop-up...

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