I am using SourceTree to commit my changes and Stash in conjunction with Jira.
Stash did recognize the JIRA ticket(s) in my commit message, so did JIRA and added the commits in the Developer section however i used the directives
#comment
#resolve
but neither of them worked. Before I did the same thing to a BitBucket repository which was linked to a JIRA Ticket, it worked without any problems. The JIRA Ticket closed as well as added my commit comment (as far as I remember)