JIRA does not deploy on websphere 6.1 when you have installed the Feature Pack for Web Services.

ADMA5016I: Installation of jira_war started.

ADMA5067I: Resource validation for application jira_war completed successfully.

ADMA5058I: Application and module versions are validated with versions of deployment targets.

ADMA5009I: An application archive is extracted at /home/was/IBM/WebSphere/AppServer/profiles/AppSrv02/wstemp/wstemp/app_120314a73df/ext

ADMA5003I: The JavaServer Pages (JSP) files in the Web archive (WAR) files jira.war compiled successfully.

ADMA5005I: The application jira_war is configured in the WebSphere Application Server repository.

ADMA5053I: The library references for the installed optional package are created.

ADMA5005I: The application jira_war is configured in the WebSphere Application Server repository.

ADMA5001I: The application binaries are saved in /home/was/IBM/WebSphere/AppServer/profiles/AppSrv02/wstemp/-228498399/workspace/cells/centos5wasNode02Cell/applications/jira_war.ear/jira_war.ear

ADMA5005I: The application jira_war is configured in the WebSphere Application Server repository.

SECJ0400I: Successfuly updated the application jira_war with the appContextIDForSecurity information.

ADMA5006E: An error occurred configuring jira_war in WebSphere Application Server repository: com.ibm.ws.metadata.annotations.AnnotationException: Annotation processing failed for class: com/atlassian/jira/issue/Bug.class

ADMA5011I: The cleanup of the temp directory for application jira_war is complete.

ADMA5014E: The installation of application jira_war failed.
The installation of application jira_war failed.

This does not happen without the feature pack.