We've had similar problems with 4.2 => 4.3 migration.
It is a migration from JBossMQ (HA-singleton) to JBMessaging.
With 4.2 we use SpyTopic/Queue to have failover.
This code must be refactored to standard JEE.
But with JBM this problems are gone.
Do you have a mixed environment with 4.2 and 5.1 running?
serveral JBoss cluster with 300+ instances sounds very huge!