It appears that our implementation of using Quartz - JDBCJobStore along with Spring, Hibernate and Websphere is throwing unmanaged threads.
I have done some readin
You will have to use websphere's managed thread pools. You can do this via spring and commonj. CommonJ can has a task executor that will create managed threads. You can even use a reference to a jndi managed thread resource. You can then inject the commonj task executor into the Spring based Quartz SchedulerFactoryBean.
Please see http://open.bekk.no/boss/spring-scheduling-in-websphere/ and scroll to "Quartz with CommonJ" section for more details.