Maybe all the other threads (JBoss) now running in the same VM are competing for resources/processor time.
Is the lost time spent in your servlet, or in Tomcat ?
If in Tomcat then you may be interested to try the JBoss/Jetty combo and compare results. Many people claim a real performance benefit, particularly under load. www.jboss.org and this forum are run by Jetty.
Provided that you are J2EE compliant you should not have to make any changes to your app. Let me know if you have any problems.