I'm also experiencing the same problem as described in this post. I have loaded the YunSerialTerminal sketch. The 32u4 works according to sketch. This means that I can see a printout in the putty console as a response to the "~0" command for example. When I press the yun rst button next to the leds I can see the usb led light when the button is pressed. But after button release nothing happens. There are no printouts in the console.
Please help me solve my problem.