What happens to a bean managed JTA transaction at timeout?

According to the documentation it is marked for rollback, but if I'm managing that transaction, and it times out or we reboot the server it is associated with a thread indefinitely. Then we get this exception:

Caused by: java.lang.IllegalStateException: BaseTransaction.checkTransactionState - ARJUNA016051: thread is already associated with a transaction!

Basically the transaction lives on that thread and is orphaned. How should I deal with this situation? We never had this issue on JBoss 4, but now that we've upgraded to JBoss EAP 6.2.3 we're experiencing the exception.