I wonder, what is the fix for Linux Plex Media Servers? There is no registry here 
For linux, itâs the preference.xml file. Why am I locked out of Server Settings and how do I get in? | Plex Support
Okay, but I do not get this permission error. The server just doesnât show up in my account. Even when I access the server IP directly.
Since you have another server, you donât see that same error since there is something to show. Not seeing your server even when it is confirmed to be running is almost always caused by the account you signed into in Plex Web not being the same that claimed the server. Please check the xml file as mentioned earlier.