Hello all
I had a similar issue: all activities completed but the course completion did not update accordingly and was showing 0 activities completed.
It was a brand new install and the problem got fixed as soon as the Moodle's cron job setup was completed.
We ran it first on the command line and then every ninute using the Cpanel cron job console as explained here:
https://docs.moodle.org/33/en/Cron_with_Unix_or_Linux
... and that's it: the course completion status is now updated as completed automatically as expected!
Thanks for pointing to the Cron issue.