@Saulius: The Ubuntu "tomcat6" package is currently not integrated with
Apache, it provides a standalone Tomcat server. We may provide a
tomcat6-apache package someday that would build-depend on tomcat6-common
and provide AJP integration.

You're right it isn't a fix but since I couldn't reproduce the issue
(and only one person seemed to experience it) it was a good workaround.
The problem is apparently linked to issues in local networking
preventing local access to hostname:8009, not really in Tomcat or its
Ubuntu packaging. If you have the same issue, could you check that your
hostname is properly resolved in /etc/hosts ? that you can access your
hostname locally on port 8009 ? Thanks.

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Tomcat fails to shutdown (can't connect to port 8009)
https://bugs.launchpad.net/bugs/299866
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