Renamed file does show as renamed. Bonus, a new file I created on the server from context menu "New text file" entry does also show on clients
Hmm... so what's different about the files that don't show up? If we can figure that out, that may point to the solution... Were they created in a notably different way (e.g. uploaded from a client)? Are they symlinked into the directory? Are they named in a notably different way? Very different in size? You've said you've already checked file permissions, but what about the actual owner/group -- are they the same as the files that do show up?
Is SELinux (or some other security software) running and doing something weird maybe? For Fedora, I think there would be a log entry at /var/log/audit/audit.log if something is getting blocked due to a security policy, but I don't run Fedora personally.