Well I just forgo this entire thing. Removed the MyServers plugin entirely and just did the forwarding via cloudfare proxy, SSL and HSTS and using Nginx Proxy.
Downside with this setup though is that it relies on the nginxproxymanager container which relies on Docker. But my machine is set up to automatically mount the array and start nginxproxy container anyway.
Would have been nice to lower level config like just relying on Unraid being running (not docker or any containers) but I didn't want to have to hack around with SSL from cloudfare for that.
I really don't like this "myservers" plugin. It isn't secure, is still in beta and even the backups are not encrypted.
OOF. It was the setting in the shares > 'share name' > Case-sensitive names: lower
Changed it to 'Auto' and it works fine. Explains why filenames with all lowercase were fine, and those with mixed case or Capital case were inaccessible.