Behold! The power of ignorance

It's looking like the bug has nothing to do with JNI.
I don't really know much about C++ threading, the Boost APIs or even STL. So I don't yet see the fundamental flaw in this event loop:

        while(true){
            if(!_eventList.empty()){

                boost::mutex::scoped_lock alock(_mutex);/*Yes Charlweed, lock is an INSTANCE.*/
                for(eventIterator =_eventList.begin();eventIterator != _eventList.end();eventIterator++){
                    /* pop the event off of the queue */
                    queuedEvent = &(*eventIterator);// This line really bugs me.
                    //processEvent(queuedEvent,javaThreadEnv,theUpperDeck);
                }
                _eventList.clear();
            }
        }

It does not work at all. Because this is running on a separate thread, I want it to flow forever, PAUSING only when it cannot get a lock on the mutex. I'm not sure what is really happening, but it looks like the other thread blocks permanently after the _eventList gains an item.
Dang.