Hmm, I can confirm that logs say nothing about stopping. I don't think
that it should be like that.

It'd seem that some times I've got the lines into my catalina.out:

Jul 21, 2011 10:09:14 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 27464 ms
Jul 21, 2011 12:35:38 PM org.apache.coyote.http11.Http11Protocol pause
INFO: Pausing Coyote HTTP/1.1 on http-80

But when I just did the stop procedure (service tomcat6 stop) and
confirmed that java process exited afterwards nothing was written out.

Perhaps you should change the bug description?

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https://bugs.launchpad.net/bugs/827922

Title:
  On Tomcat6 shutdown web apps do not get shutdown

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