Deleting jobs as the root user is perfectly fine. Submitting jobs as root should be avoided. The root account on the server node is always considered a manager.
For compute-0-6, please confirm you can communicate with from the server node. First try to ping it, then try to ssh to it. PBS Pro can’t function properly if your network isn’t working.
For your other compute nodes, please confirm that you can ssh back and forth with the server without a password as the user submitting jobs.
This post may help: Qstat: cannot connect to server amaster (errno=113)