Are you using @In EntityManager? or @PersistenceContext EntityManager?
The SMPC is conversation-scoped, ejb-container managed PC is not...
although this is not a LIE I guess, but sounds similar...
I'm using Seam POJO components, entityManager is injected via @In.
I don't know if the EJB3 can be developer with seam hotdeploy, so I using only POJO components.
Please provide the entire stack trace.