Automatic branch detection is unable to create link to JIRA automatically

Problem Description

If Bamboo has branch name with JIRA issue key included in its name, as long as there's an Application Link between Bamboo and JIRA, the link between the Bamboo plan and JIRA Issue will be established automatically.

However if for Automatic branch detection in Bamboo, it won't create the link straightaway in JIRA. Instead, it will just create the Link in Bamboo to JIRA but not from JIRA to Bamboo. It will show a button like the following screenshot.

The following warning message will be generated in Bamboo log.

2013-06-13 18:35:42,270 WARN [1-BranchJiraLinkingBackgroundThread:pool-4-thread-2] [JiraBranchLinkingServiceImpl] Could not create remote issue link from issue 'TEST-3' to plan branch 'TEST project - Plan Github - TEST-3'. No matching JIRA project could be found on any linked JIRA Server.

Most probably Bamboo is looking for similar Project name in JIRA. Nevertheless, this behaviour didn't happen when the Branch is created manually, or added manually from the detected branch from Create Branch button.

How it should work

It should create a link automatically from JIRA. Just like when it's added manually from Create Branch button. Just like the following screenshot.

This is replicated on JIRA 6.0.2

Steps to replicate the issue

1. Establish an Application Link between JIRA and Bamboo.
2. Make sure the Application Link works fine. You could achieve this by commenting JIRA Issue key on Bamboo Build and see if it will be linked to JIRA.
3. Create a test repository and a branch and name the branch with JIRA Issue Key.
4. On Plan Configuration, choose Branches and make sure Automatically manage branches is checked.
5. Wait and see until the branch is added.
6. On Bamboo Plan switch to the branch which the name is similar with JIRA Issue Key.

Workaround

Create a user SYSTEM in Jira internal directory.