I believe I have solved the issue. I was able to log back in, and apply the changes on one of the files affected. So far it looks like it's working on both my test environment and your server as well.
Currently when checking through the custom field groups, the plugin performs an additional sub-query to see if the given custom field is defined for the actual post/page. If there is no record of the custom field, then the post/page is considered as a potential result. If there is a record of the custom field with the post, then the normal check is performed as before. So it still filters, but only the ones which have the custom fields defined – and leaving the ones without the custom fields defined in the filters.Best,
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