I'm confused what's happening here - are you doing email alerts based on JMX properties? And you rebooted, and alerts wouldn't start?
If that's the case, I think you just have a dependency issue here. Your alert depends on the ESB being deployed, and the server may be trying to deploy the alert first. Can you paste your alert mbean XML? If you add the ESB deployment to the deployment-list, that should solve the problem.