We had a similar message recently. We couldn't get the external database plugin to create new courses because of this error occuring. Although it's a different context, we discovered our problem was caused by the main admin user account being removed by someone from the list of "site administrator" roles. And thus, the cron's "user" didn't have site administrator permissions.
So perhaps check that the site administrator user, is actually a site administrator. Might be one you've already covered, but just thought I might share!
So perhaps check that the site administrator user, is actually a site administrator. Might be one you've already covered, but just thought I might share!