Always use MSCS to manage clusters

Do not try to perform start and stop operations directly on any queue manager under the control of MSCS, using either the control commands or the IBM® WebSphere® MQ Explorer. Instead, use MSCS Cluster Administrator to bring the queue manager online or take it offline.

Using the MSCS Cluster Administrator is partly to prevent possible confusion caused by MSCS reporting that the queue manager is offline, when in fact you have started it outside the control of MSCS. More seriously, stopping a queue manager without using MSCS is detected by MSCS as a failure, initiating failover to the other node.