Taking and examining several thread dumps should show you where the application is spending its time. Unfortunately, you are running the app server as a service and I don't know of any way on Windows 2003 to send a SIGQUIT signal to a service (if you ran the app server from a command prompt you could type CTRL-BREAK in the command window to get the thread dump). You could try connecting JConsole to the app server, see the JConsole documentation for instructions on how to do this. JConsole provides a thread dump feature.
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