I just opened my v2 that I bought. I installed all the drivers, and everything looks alright, however the configuration utility fails to run.
I tried restarting, changing the cable, changing a usb port, reinstalling drivers, running as administrator, plugging in and out. Nothing seems to work. Also, nothing is using the device and no other programs are running.
I am sorry you are not able to connect to your AVR programmer v2. Can you verify that you are running only a single instance of the Pololu USB AVR Programmer v2 Configuration Utility? If you are, it sounds like there could be something like another program trying to use your USB ports on startup. If that is the case, you might try using another computer (ideally one not loaded with similar programs as the one you are currently try to use). Otherwise, you would have to do something like try finding out what is using those USB ports and disable them.