root should never have servers, though. That is a huge security concern.
From the Python wiki:
Creating Servers
Servers may only be created by unprivileged users, or in other words: not root. Be sure to log in as any unprivileged user to create any servers you wish; trying to create a server as root will be met with instructions on how to create additional users from the command line.
From the NodeJS wiki:
Creating Servers
Servers may only be created by unprivileged users, or in other words: not root. Be sure to log in as any unprivileged user to create any servers you wish and leverage group membership to share control of servers with others!
So the best plan of action now is simply to chown those root-owned servers to non-root and use that user in the webui.
chown -R will:will /var/games/minecraft/{servers,backup,archive}/myservername