I found this in the manual for WinAVR, I think it will help answer a lot of problems people have sometimes:
LibUSB-Win32 is a USB library that is linked into AVRDUDE and AVaRICE to allow them to connect to the Atmel JTAG ICE mkII and the Atmel AVRISP mkII. Drivers for these devices are also included. LibUSB is installed under:
The drivers for the JTAG ICE mkII and the AVRISP mkII are also located in the above directory.
To install the LibUSB-Win32 drivers (when AVR Studio is not installed): - Plug in your Atmel device (JTAG ICE mkII or AVRISP mkII). - When Windows asks to locate drivers for this device, select "Install from a list or specific location". Press Next. - Uncheck the checkbox, "Search removable media". - Check the checkbox "Include this location in the search" and select the location of the drivers in the directory specified above. Press Next. The driver will then be installed.
AVR Studio can install and use the USB drivers from Jungo (which is included as part of the AVR Studio installation). However, the Jungo drivers and the LibUSB-Win32 drivers are mutually exclusive; if one set is installed the other set will not work.
You can uninstall the driver by plugging in the device (and making sure it is powered on), use the Device Manager to find and select the device (under Jungo or LibUSB-Win32, depending on which driver is installed), right click and select "Uninstall". Then, install the other driver according to the correct procedures.
LibUSB also has a "filter" driver that is available, however, using this is not recommended by the LibUSB author.