Well, first of all which OS did you use??
Next is get yourself the little tool "ATMEL Flip". Install it and then put in you JB stick with button pressed while stick in. Then release the button and install the drivers for your at90usb. You can find them in c: programs/atmel/USB. There are the Driver package you will need.
If you run a 64bit OS you have to sign the atmel usb drivers first and then dissable driver signature enforcement, easy todo with little tool "dseo", its an overrider so you can open up your at90usb162 in atmel.