@alspad - Does a device show up on the USB when you plug it in? On windows it should be a COM port, I think in mac it should be in /dev/tty something.
ssh into the Yun and execute reset-mcu, does yellow RX let blink after 1-2 seconds?
This does sound like the 32u4 has problems, what shields or other devices have you plugged in?
@quiggers & @ geezerengineer -Your symptoms are quite different from the original poster's, if you describe your symptoms in a separate thread it will make it easier for people to help you.