Hi,
Thank you for the details, it helps a lot!
I checekd the configuration, and I can see a few exclusions by tags and other taxonomies as well under the Advanced options: https://i.imgur.com/5vwmJvZ.png
When I tried the filters, the items missing seemed to be belonging to those tags excluded. If you remove the unwanted exclusions, it should very likely resovle the issue.
