Could you please try the following:
- Start the Java program
- Hold down the Due RESET button, and keep it held down
- Select the Due serial port from the menu in the java program
- Wait a few seconds for a few "No response" messages
- Release the RESET button
When I do this, the program appears to run normally.
I think the problem is the same as the one we have noticed here before - when the serial port is opened the Due sends a few lines of serial output, then resets, then starts again. I don't think that problem is solved yet.