I've found out what's the problem with failing test, this finally block should be like this:

finally {
         em2.getTransaction().commit();
         em2.close();
         latch.countDown();	// signal that tx2 is committed
}

I think, we should close em2 before we send the signal, because sometimes em2 appears to be opened after the test completion -> releaseUnclosedEntityManagers() is invoked, but in the meantime em2 is closed in the finally block in another thread.