Problem is that the AMQMessageStore is closed but not removed from the cache inside the PersistenceAdapter. Next time a Queue (or Topic) is created it gets the stopped and unusable message store from the cache.
After chatting with Hiram on the dev list I think introducing methods to remove the message store from the persistence adapter is the best way forward.
Looking at svn history this problem was introduced in the fix for
AMQ-1842, rev 729939, where the calls to stop the MessageStore were introduced.