When stash (v3.1.3), bamboo (v5.6.0) and JIRA are linked, with automatic branch creation configured, bamboo doesn't link issues mentioned in commit messages that are pushed with the branch creation.

To reproduce:

1. Create a JIRA issue (TEST-1)
2. Create a new repository in stash. Make sure it has a file in it (so that master exists)
3. Create a bamboo build plan for the new repo, with automatic branch creation configured
4. in the new repo, run:

• git checkout -b TEST-1-branch
• echo "TEST" > test.txt
• git add test.txt; git commit -m 'TEST-1 message' test.txt
• git push --all
  5. Wait for bamboo to pick up the change and run a build

In Stash, the commit is linked to TEST-1 (and the commit and branch show up in JIRA).

However, in Bamboo the 'issues' tab (http://localhost:6990/bamboo/browse/TEST-TEST10/issues) doesn't show any linked issues, and JIRA doesn't show a build status.

A subsequent checkin (ie "echo X > test.txt; git commit -m 'TEST-1 msg' test.txt; git push") causes this to work as expected, and the link then shows up.