The startServer.sh or stopServer.sh commands fail to start or stop the server when the server definition is part of the configuration repository.
startServer.sh webserver1 -nowait
stopServer.sh webserver1 -nowait
If none of these steps fixes your problem, check to see if the problem has been identified and documented by looking at the available online support (hints and tips, technotes, and fixes). If you don't find your problem listed there contact IBM support.