I had a similar issue where my solution was on shutdown to call System.exit() if tomcat did not shutdown in a pre-configured amount of time (which can be turned off for embedded apps). This way it works for windows too.
Here is the bug report with patch: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=17000
There problem appears when a webapp which embed some long running code is stopping but after 1 or 2mn.
There is no way to know when the tomcat will really stop and since there is sometime URGENT need to shutdown quickly tomcat, the new catalina.sh will export in the file pointed by CATALINA_PID the pid of the main java process.
So in case of urgence :
read kpid < $CATALINA_PID kill -9 $kpid
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