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When running a filter containing the JQL function PortfolioChildrenOf, different users see different results. Both users have portfolio access, and browse access to the project. Is there another permission a user needs in order to return results for this JQL function?
I would expect that the issue is surrounding project permissions. In my experience, this is almost always the issue. It's also possible that there are security levels configured on some projects restricting access.
If it were me, I would try choose a specific user, identify an issue returned by the filter that the specific user cannot see in the results, and have them try to access the issue directly with a link.