Indeed, I am not running under linux, but under Win 7 64 bits. Anyway I have a VM installed with Ubuntu. I'll check the thread and see if I can launch the Kindle with the k3flasher.
On the other hand, I'll try also to reconnect the USB, although I am not clear at what point I have to do it. When the ATK says "waiting for the USB"? I think this option would not work because in this case, the device would be in fastboot mode, right? And if so, would appear on another ATK's error message that comes out when we do not enter fastboot "Connection error. Please, reset the board and make sure the board in bootstrap mode". (sorry if it's silly what I'm saying)