Hi Phil,
It was not that, the index table is not related to the user search. The issue was the filter. That custom field is not set for users, which have a public profile, but the search does not know that, it only checks if the value is not 1. I have enabled this option, to bypass the filter on cases, where the field does not exist: https://i.imgur.com/ZBE4RED.png
It should be okay now.