I think it would behoove you to include a snippet of your code.
From your description its difficult to get a good grasp of what
you are actually doing.
So, the best response your going to get is just some random
guesses.
Maybe just post the portion where you are doing the actual reading
to start with.

To make things easier here is the code of the method run of the
looping thread :

            StringBuffer outgoingBuffer;
            List<Message> incomming;
            while (running) {
                try {
                                       // Count the number of
messages the outgoing queue has
                    int messageCount = outgoing.size();
                    outgoingBuffer = new StringBuffer();
                    for (int i=0;i<messageCount;i++) {
                        outgoingBuffer.append(new
String(parser.serialize(outgoing.poll())));
                    }
                    out.write(outgoingBuffer.toString().getBytes());

                    int availableBytes = in.available();
                    byte[] toDeserialize = new byte[availableBytes];
                    in.read(toDeserialize);
                                       // Use parser to serialize/
deserialize message (from/to JSON)
                    incomming = parser.deserialize(toDeserialize);
                    if (incomming.size()>0) {
                        System.out.println("server: "+new String(toDeserialize));
                        for (Message message:incomming) {
                                                       // Send all
registered messageListeners the message that has been received.
                            eventManager.fireEvent(message);
                        }
                    }
                    Thread.sleep(100);
                } catch(SocketException e) {
                    for (int i=0;i<CONNECTION_ATTEMPTS;i++) {
                        try {
                            System.out.println("Attempt to connect...");
                            disconnect();
                            parser.reset();
                            connect(hostname,port);
                            out.write(parser.serialize(createRecoveryMessage()));
                            System.out.println("Connected!");
                            break;
                        } catch(Exception e1) {
                            e1.printStackTrace();
                            try { Thread.sleep(1000); } catch(InterruptedException e2) {}
                        }
                    }
                } catch(IOException e) {
                } catch(InterruptedException e) {

                }
            }
            try {
                socket.close();
            } catch(IOException e) {e.printStackTrace();}
        }

Hmm. I guess WireShark ties in only at the LAN driver level.  It might
be fairly easy to round up some old beater of a machine to run on a
LAN so you can monitor traffic. Perhaps one of the other sniffers will
intercept local traffic. see http://mindprod.com/jgloss/sniffer.html

I remember years ago working with a Norton virus monitor.  It set up a
proxy mail server on your machine that simply relayed traffic through
to the real mail server.  A protocol sniffer might work like that,
forcing you to talk to a dummy address which then talks to the real
address.