JIRA when integrated with Bamboo (with the JIRA Bamboo plugin) must have access to Bamboo on startup. This is a limitation of the Bamboo plugin.
If JIRA and Bamboo are in the same instance of Tomcat, there is no way to ensure that Bamboo will start first (Tomcat does not support this)
Further, if Bamboo is not yet started, but is installed on that instance of Tomcat, JIRA's request to Bamboo will block JIRA from starting up at all. This will not happen if Bamboo is on another instance.
Here's the bug in JIRA, but the problem lies in the Bamboo plugin.