Issues not closed automatically based on commit message

Today I had an issue which wasn't closed by "Closes #573" message. A few days ago it worked without any problem.

Check to be sure that you have the issue service enabled in your repository services section. It is automatically turned on by default, but it is possible to disable it. If this isn't your issue, please raise a support request to support.atlassian.com

Issue service was enabled, but disabling and enabling it again seemed to do the trick. Perhaps some random settings problem after recent site updates.