I'm using jira-plugin version 1.3 in combination with a mercurial repository. The plugin is being used purely to provide links to JIRA items, it has not been configured to alter the JIRA item. Sometimes (but not every time) when a user pushes any number of commits, the repository on disk will be updated (the changes can be pulled by other users) but SCM Manager is apparently unaware of the change. Clicking on the Commits link shows an older version of the commit log.
The problem can be fixed by removing the JIRA configuration for the repository. SCM Manager's view of the repository then updates immediately.
I have been unable to find any errors in SCM Manager's log files. However, the line sonia.scm.repository.xml.XmlRepositoryManager - modify repository <repo> of type hg does not appear when the commit is made, instead appearing when the JIRA configuration has been removed.
I have temporarily disabled the plugin, but it would be nice to get the links working again.