JIRA does not shut down fully

After running ./bin/startup.sh and ./bin/shutdown.sh, one thread from JIRA is still left running. It appears JOTM is holding onto a database connection or something. Doing a kill -s SIGQUIT on this process lists the following thread dump:

Full thread dump Java HotSpot(TM) Client VM (1.4.2-b28 mixed mode):

"DestroyJavaVM" prio=1 tid=0x08799f80 nid=0x6f68 waiting on condition [0..bfffc274]

"Thread-6" daemon prio=1 tid=0x080fef88 nid=0x6f68 in Object.wait() [5a876000..5a876c18]
at java.lang.Object.wait(Native Method)

• waiting on <0xFull thread dump Java HotSpot(TM) Client VM (1.4.2-b28 mixed mode):

"DestroyJavaVM" prio=1 tid=0x08799f80 nid=0x6f68 waiting on condition [0..bfffc274]

"Thread-6" daemon prio=1 tid=0x080fef88 nid=0x6f68 in Object.wait() [5a876000..5a876c18]
at java.lang.Object.wait(Native Method)

• waiting on <0x451001c0> (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
  at java.lang.Object.wait(Object.java:429)
  at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:595)
• locked <0x451001c0> (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
  at java.lang.Thread.run(Thread.java:534)

"Thread-3" prio=1 tid=0x080d9f38 nid=0x6f68 in Object.wait() [5a3f6000..5a3f7098]
at java.lang.Object.wait(Native Method)

• waiting on <0x4616b200> (a org.enhydra.jdbc.pool.PoolKeeper)
  at org.enhydra.jdbc.pool.PoolKeeper.run(PoolKeeper.java:50)
• locked <0x4616b200> (a org.enhydra.jdbc.pool.PoolKeeper)
  at java.lang.Thread.run(Thread.java:534)

"Thread-2" prio=1 tid=0x087f7f70 nid=0x6f68 waiting on condition [5a376000..5a377118]
at java.lang.Thread.sleep(Native Method)
at org.hsqldb.Log.run(Unknown Source)
at java.lang.Thread.run(Thread.java:534)

"JonasClock" daemon prio=1 tid=0x087c9538 nid=0x6f68 waiting on condition [5a2f7000..5a2f7198]
at java.lang.Thread.sleep(Native Method)
at org.objectweb.jonas_timer.TimerManager.clock(TimerManager.java:142)
at org.objectweb.jonas_timer.Clock.run(TimerManager.java:46)

"JonasBatch" daemon prio=1 tid=0x08129f28 nid=0x6f68 in Object.wait() [5a277000..5a277218]
at java.lang.Object.wait(Native Method)

• waiting on <0x45e95e58> (a java.util.Vector)
  at java.lang.Object.wait(Object.java:429)
  at org.objectweb.jonas_timer.TimerManager.batch(TimerManager.java:193)
• locked <0x45e95e58> (a java.util.Vector)
  at org.objectweb.jonas_timer.Batch.run(TimerManager.java:65)

"Signal Dispatcher" daemon prio=1 tid=0x080a5b58 nid=0x6f68 waiting on condition [0..0]

"Finalizer" daemon prio=1 tid=0x08091050 nid=0x6f68 in Object.wait() [58ac8000..58ac8598]
at java.lang.Object.wait(Native Method)

• waiting on <0x45bc0138> (a java.lang.ref.ReferenceQueue$Lock)
  at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:111)
• locked <0x45bc0138> (a java.lang.ref.ReferenceQueue$Lock)
  at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:127)
  at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=1 tid=0x08090460 nid=0x6f68 in Object.wait() [58a48000..58a48618]
at java.lang.Object.wait(Native Method)

• waiting on <0x45bc01a0> (a java.lang.ref.Reference$Lock)
  at java.lang.Object.wait(Object.java:429)
  at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:115)
• locked <0x45bc01a0> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=1 tid=0x0808f160 nid=0x6f68 runnable

"VM Periodic Task Thread" prio=1 tid=0x080a8400 nid=0x6f68 waiting on condition
"Suspend Checker Thread" prio=1 tid=0x080a5170 nid=0x6f68 runnable
451001c0> (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Object.wait(Object.java:429)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:595)

• locked <0x451001c0> (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
  at java.lang.Thread.run(Thread.java:534)

"Thread-3" prio=1 tid=0x080d9f38 nid=0x6f68 in Object.wait() [5a3f6000..5a3f7098]
at java.lang.Object.wait(Native Method)

• waiting on <0x4616b200> (a org.enhydra.jdbc.pool.PoolKeeper)
  at org.enhydra.jdbc.pool.PoolKeeper.run(PoolKeeper.java:50)
• locked <0x4616b200> (a org.enhydra.jdbc.pool.PoolKeeper)
  at java.lang.Thread.run(Thread.java:534)

"Thread-2" prio=1 tid=0x087f7f70 nid=0x6f68 waiting on condition [5a376000..5a377118]
at java.lang.Thread.sleep(Native Method)
at org.hsqldb.Log.run(Unknown Source)
at java.lang.Thread.run(Thread.java:534)

"JonasClock" daemon prio=1 tid=0x087c9538 nid=0x6f68 waiting on condition [5a2f7000..5a2f7198]
at java.lang.Thread.sleep(Native Method)
at org.objectweb.jonas_timer.TimerManager.clock(TimerManager.java:142)
at org.objectweb.jonas_timer.Clock.run(TimerManager.java:46)

"JonasBatch" daemon prio=1 tid=0x08129f28 nid=0x6f68 in Object.wait() [5a277000..5a277218]
at java.lang.Object.wait(Native Method)

• waiting on <0x45e95e58> (a java.util.Vector)
  at java.lang.Object.wait(Object.java:429)
  at org.objectweb.jonas_timer.TimerManager.batch(TimerManager.java:193)
• locked <0x45e95e58> (a java.util.Vector)
  at org.objectweb.jonas_timer.Batch.run(TimerManager.java:65)

"Signal Dispatcher" daemon prio=1 tid=0x080a5b58 nid=0x6f68 waiting on condition [0..0]

"Finalizer" daemon prio=1 tid=0x08091050 nid=0x6f68 in Object.wait() [58ac8000..58ac8598]
at java.lang.Object.wait(Native Method)

• waiting on <0x45bc0138> (a java.lang.ref.ReferenceQueue$Lock)
  at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:111)
• locked <0x45bc0138> (a java.lang.ref.ReferenceQueue$Lock)
  at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:127)
  at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=1 tid=0x08090460 nid=0x6f68 in Object.wait() [58a48000..58a48618]
at java.lang.Object.wait(Native Method)

• waiting on <0x45bc01a0> (a java.lang.ref.Reference$Lock)
  at java.lang.Object.wait(Object.java:429)
  at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:115)
• locked <0x45bc01a0> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=1 tid=0x0808f160 nid=0x6f68 runnable

"VM Periodic Task Thread" prio=1 tid=0x080a8400 nid=0x6f68 waiting on condition
"Suspend Checker Thread" prio=1 tid=0x080a5170 nid=0x6f68 runnable