Recently I noticed with another user that they had blocked a domain and it, for some reason, was hiding all comments in the thread despite the blocked domain being completely unrelated to the post (the post wasn't on that domain, wasn't by someone on that domain, and no commenters were from that domain).
If posts are disappearing when you're logged in but not when logged out, it should be something like that: either a language filter, federation turned off, or a blocked community you might not expect filtering it out. You can double check by unblocking domains/magazines to see if any of them return comments, though that might be troublesome with many blocked.