I programmed the m16u2 with the following command (which I have used in the past), I the output seems fine to me.
L:>avrdude -p m16u2 -c avrisp -v -P COM5 -b 19200 -U flash:w:Arduino-usbserial-atmega16u2-Mega2560-Rev3.hex
avrdude: verifying ...
avrdude: 4034 bytes of flash verified
avrdude: safemode: lfuse reads as EF
avrdude: safemode: hfuse reads as D9
avrdude: safemode: efuse reads as F4
avrdude: safemode: Fuses OK (E:F4, H:D9, L:EF)
but then when I connect the arduino to the computer; the computer does not recognized the port at all.
I confirmed that the cable and USB port are good.
So... the chip seems to be alive because I can program it using the avrdude command.... but why then the computer cannot find it when I connect it via the USB cable? Not even as a libusb-win32 device.