We have tomcat6 deployed for multiple servers running our inhouse apps
and have no shutdown problems.

What applications are you running? Could you do a jstack printout* AFTER
you've called service tomcat6 stop? Does tomcat accept new connections
or multiple SHUTDOWN requests after running the service tomcat6 stop for
the first time?

Note that you'll need to run jstack as the tomcat user, with extra
arguments to compensate for java.io.tmpdir, for example:
"-J-Djava.io.tmpdir=$WHEREEVER_YOUR_TOMCAT_TEMP_IS".

For one of my installations its:

$ sudo -u tomcat jstack -l -J-Djava.io.tmpdir=/tmp/tomcat6-tmp
<tomcatPid>

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

Title:
  On Tomcat6 shutdown web apps do not get shutdown

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