When I sit at the lights in gear I am getting a louder than normal vibration sound. If I go into neutral I loose it and goes back to normal diesel sound.
If the noise changes as you speed up/slow down, I'd suggest you have a bad motor mount. When these wear out, they tend to do exactly as you're suggesting which is make noise as you have it in gear. The engine torques over, connecting the engine to the frame and makes noise. When you put it in neutral, the engine goes back to a "resting" state and no more noise. As you speed up/slow down, the mount is continually connecting/disconnecting with the frame, so the noise comes and goes. You'll most probably experience it as you speed up. You may also hear a slight clunking sound as it shifts gears.