I've been getting this message, haphazardly, in IE8 and Firefox, running 1.6.0_22. It seems it's produced by this code:
// FIXME: need more messages
// Consider throwing an InternalError here since this would be entirely our fault
System.err.println("sun.plugin2.main.client.PluginMain: unrecognized message ID " + msg.getID());
It seems to be about communication with the browser through LiveConnectSupport.
It doesn't seem to do anything bad, but it's disconcerting.