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If anyone is still interested, we modified ManagedConnectionFactoryDeployment like so and the issue was resolved:

   private synchronized ManagedConnection open(Subject s) throws ResourceException {
             if (recoverMC == null) {
                       recoverMC = createManagedConnection(s, null);


                       return recoverMC;
             }


             boolean valid = true;
             if(recoverMC instanceof BaseWrapperManagedConnection) {
                       valid = ((BaseWrapperManagedConnection) recoverMC).checkValid();
             }


             if(! valid) {
                       log.info("open - recoverMC is not valid, reopening for deployment: " + toString());
                       close(recoverMC);
                       recoverMC = createManagedConnection(s, null);
             }
             
             return recoverMC;
   }

Also nulled out recoverMC in the stopService method:

   protected void stopService()
   {
      if (recoveryRegistered)
      {
         if (getXAResourceRecoveryRegistry() != null)
         {
            close(recoverMC);


            getXAResourceRecoveryRegistry().removeXAResourceRecovery(this);
            recoveryRegistered = false;


            if (log.isDebugEnabled())
               log.debug("Unregistered for XA Resource Recovery: " + dmd.getJndiName());
         }
      }


            recoverMC = null;
      mcf = null;
      mcfClass = null;
   }