Within the context of a One-to-Many relationship, NamedQueryCollectionInitializer .initialize() never actually populates the PersistantBag on the parent after it calls query.setCollectionKey( key ).setFlushMode( FlushMode.MANUAL ).list() to retrieve the children.

This is documented in the forums here: http://forums.hibernate.org/viewtopic.php?t=986428

Additionally, the poster has a fix posted which may solve the problem, or at least lay out the groundwork for a solution. Here is the proposed implementation of NamedQueryCollectionInitializer.initialize():

public void initialize(Serializable key, SessionImplementor session)
throws HibernateException {

if (log.isDebugEnabled()) {
log.debug("initializing collection: " + persister.getRole()
+ " using named query: " + queryName);
}

// TODO: is there a more elegant way than downcasting?
AbstractQueryImpl query = (AbstractQueryImpl) session
.getNamedSQLQuery(queryName);
if (query.getNamedParameters().length > 0) {
query.setParameter(query.getNamedParameters()[0], key, persister
.getKeyType());
} else {
query.setParameter(0, key, persister.getKeyType());
}

List list = query.setCollectionKey(key).setFlushMode(FlushMode.MANUAL)
.list();

// Uh, how 'bout we save the collection for later retrieval?
CollectionKey collectionKey = new CollectionKey(persister, key, session
.getEntityMode());
for (Object object : session.getPersistenceContext()
.getCollectionsByKey().keySet()) {
if (collectionKey.equals(object)) {
PersistentCollection persistentCollection = session
.getPersistenceContext().getCollection(collectionKey);

Serializable[] serializables = new Serializable[list.size()];
for (int i = 0; i < list.size(); i++) {
serializables[i] = persister.getElementType().disassemble(
list.get, session,
persistentCollection.getOwner());
}

persistentCollection.initializeFromCache(persister,
serializables, persistentCollection.getOwner());
persistentCollection.setSnapshot(key, persistentCollection
.getRole(), serializables);

persistentCollection.afterInitialize();

session.getPersistenceContext().getCollectionEntry(
persistentCollection).postInitialize(
persistentCollection);
}
}
}