Not all eligible users are sent a notification when notify is run using Cron

So far, from what we have discovered, it looks like when sending via Cron, Notify does send notifications to use who have the administrator role, but not users who don't have that role, for example authenticated users, this is despite all roles having the "access notify" permission.

I'm now wondering if this code could be causing the issue, notify.module:_notify_send():

          // Skip to next if user is not allowed to view this node.
          if (!$userobj->hasPermission('administer nodes') && 0 == $node->isPublished()) {
            continue;
          }
          if (!$userobj->hasPermission('administer nodes') && !in_array($node->getType(), $defaultlist)) {
            continue;
          }

            if (!$userobj->hasPermission('administer comments') && 0 == $commobj->isPublished()) {
              continue;
            }
            if (!$userobj->hasPermission('administer comments') && !in_array($node->getType(), $defaultlist)) {
              continue;
            }
            if (!$config->get('notify_unpublished') && 0 == $commobj->isPublished()) {
              continue;
            }
            // Determine whether to show comment status.
            if ($userobj->hasPermission('administer comments')) {
              $status = $commobj->isPublished() == 1 ? t('[Published]', array(), array('langcode' => $upl)) : t('[Unpublished]', array(), array('langcode' => $upl));
            }
            else {
              $status = '';
            }

Ok, specifically what additional information do you need?

Based on #3 there's clearly a mismatch between what the code does and what the comment says, which could very well be the problem here.