When a commit in a subproject references an issue in the parent, a comment from Anonymous is added to the issue that says: "Applied in changeset commit:90812738092374"

There should also be a project identifier in the comment, so the reference hyperlinks correctly: "Applied in changeset subproject-identifier:commit:90812738092374"

This behavior was observed on Redmine 1.3.0.stable.8692. The parent project has no repository and the child is associated to a mercurial repository. In the global Redmine configuration section "Repositories > Referencing and fixing issues in commit messages" the setting "Applied Status" is set to "Resolved" and "% Done" is set to "100 %".

Other version information:

$ RAILS_ENV=production ruby script/about
About your application's environment
Ruby version              1.8.7 (i686-linux)
RubyGems version          1.6.2
Rack version              1.1.3
Rails version             2.3.14
Active Record version     2.3.14
Active Resource version   2.3.14
Action Mailer version     2.3.14
Active Support version    2.3.14
Application root          /var/www/redmine
Environment               production
Database adapter          mysql
Database schema version   20110902000000
$ mysql --version
mysql  Ver 14.14 Distrib 5.1.41, for debian-linux-gnu (i486) using readline 6.1
$ hg --version
Mercurial Distributed SCM (version 2.1)