I think you are a little confused and skipped a step after upgrading.
In the past the backup before update was only possible if you would use Admin Tools' Joomla! Update feature. It wasn't a plugin. On the downside you could not use Joomla! Update to update your site if you wanted a backup. That was a stupid decision on my part because you needed two of my extensions (Akeeba Backup and Admin Tools) to update your site.
When I removed the update feature from Admin Tools I added the backup before update feature to Akeeba Backup. There it is implemented as a system plugin and works with Joomla! Update. Since this is a new feature in Akeeba Backup the new plugin is disabled by default. After the update you must go to Components, Akeeba Backup. This displays the Post-Installation page which asks you to enable this new plugin. It's up to you to decide if you want to accept the default and enable the plugin, or if you want to disable it. But you must go through that page and press the Apply Settings button. The trick is that by pressing the button you are simultaneously accepting responsibility of enabling this feature. Apparently you didn't do that step on your sites.
Nicholas K. Dionysopoulos
Lead Developer and Director
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