I am guessing somewhat but I believe what you have is a cmd_port file that still exists and hitting a port that is listening but is not an actual cloverleaf port. A “proper” shutdown during the reboot cycle and the elimination of a process actually listening on that port is probably what is cleaning things up. It is likely that you would do fine by doing a manual cleanup of all cmd_port, pid, and wpid files associated with the site. Just my 2 cents, hope it helps.
