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Instruction (https://confluence.atlassian.com/display/BAMBOO044/Running+Bamboo+service+on+Windows+as+the+local+user) could be updated: display name from "Bamboo build server" to "Atlassian Bamboo Bamboo".
How did you try to add it as a service?
If you just ran the installer according to the docs, what error did you get when it tried to add it as a service?
You'll need to adjust your environment so that it points to the right version of Java, the one built into the Jira installation. Set the JAVA_HOME variable to the root of the jre in the Jira installation, and make sure $JAVA_HOME/bin is in the path before the system installed Java, then run the batch file again.