This seems to be intentional. As a result, my developers need to include the issue key in each commit to a feature/hotfix/bugfix branch, and then I must add it AGAIN when I merge their branch into a development trunk.
I've got that "I'm doing it wrong" feeling, but I've found quite a few posts on these forums with the same problem, and this seems like an obvious inefficiency.
Stash is creating my branches, from Jira, and naming them per Stash's naming conventions. I'm surprised that Bamboo cannot map the builds back to the JIRA issues that it addresses, without explicitly noting them in commit messages.
HALP, what am I missing?
EDIT: according to this: https://confluence.atlassian.com/display/BAMBOO057/Using+plan+branches#Usingplanbranches-configurebranch the commit message should not be necessary, at least for the linking of plan branches back to JIRA issues.