Thanks for the suggestions, I tried the beginCall() ... endCall() on the 
lifecycle and yes that does work, I can get an EntityManager in my thread 
however back to the original problem, the entity manager has not started a 
transaction for me, so nothing gets posted to the db and when I flush I get


  | 23:15:43,708 ERROR [STDERR] Exception in thread "Thread-21" 
  | 23:15:43,708 ERROR [STDERR] javax.persistence.TransactionRequiredException: 
no transaction is in progress
  | 23:15:43,708 ERROR [STDERR]     at 
org.hibernate.ejb.AbstractEntityManagerImpl.flush(AbstractEntityManagerImpl.java:293)
  | 23:15:43,708 ERROR [STDERR]     at 
org.jboss.seam.persistence.EntityManagerProxy.flush(EntityManagerProxy.java:90)
  | 23:15:43,708 ERROR [STDERR]     at 
model.EXAccessPoint.flushToDb(EXAccessPoint.java:236)
  | 23:15:43,708 ERROR [STDERR]     at 
model.EXBackgroundThread.run(EXBackgroundThread.java:36)
  | 23:15:44,282 INFO  [EXAccessPoint] calculateEx():from=11:15:39 
PM;now=11:15:44 PM;exs.size()=3;currentStartIndex=2
  | 

The code inside the thread does this at the moment


  | Lifecycle.beginCall();
  | EntityManager em = (EntityManager)Component.getInstance("em", true);
  | ...
  | em.persist(...);
  | ...
  | em.flush();
  | Lifecycle.endCall();        
  | 

I'll try JNDI directly...

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