I have an Arduino Uno version 2 which was working but now is not detected in Device Manager.
The same cable works my AVRISP mk 11 fine and this device is detected.
I can program the ATmega328 via the ISP connection but I need the USB link for debugging.
I don't think it's a code issue because the actual device that Windows sees is not the 328, it's the FTDI chip; although there's a chance that the FTDI chip is being very picky and waiting for a handshake from the 328 before appearing to the host. What happens if you (carefully) remove the 328 from its socket and then plug in the USB?
If you have any other Uno boards, try swapping the 328 and see if it works on the other one. Make sure you're using the drivers that came with the Arduino environment download. Try it on another computer as well.
EDIT: I'd also suggest rebooting Windows. I've seen it do funky unexplainable things that went away with a simple reboot.
EDIT 2: Are you using a USB hub? If so, is it powered externally? If not, there's a chance that the Uno isn't getting enough power to start up.
The USB to Serial functionality is performed by the 8U2 on the UNO Rev2. It's possible the firmware on the 8U2 has been corrupted and needs to be reloaded.
The 8U2 can be put into a mode, called DFU mode, that will allow you to upload new firmware.
You can can find more detailed instructions for uploading new firmware to the 8U2 here: DFUProgramming8U2
There is also another ISP header for the 8U2 near the 8U2 that you could use to load the new firmware with your AVRISP mk 11.
Try connecting the Arduino to the cable and pressing the reset button on the Arduino. Unplug the reattach. If the board's last sketch was stuck on a logic error, i.e. a never ending loop, it may be incorrectly recognized.
