When running the soitoolbox utility against a clustered SOI install you will need to first manually turn off all the SOI cluster resource groups. This is because the soitoolbox is not cluster aware, it will try to shut down the SOI servers services it knows of that you configured in the soitoolbox.cfg configuration file. Since the services are part of a cluster group the cluster will to try to bring up the services is the SOI resource group back online.