I might not be much help, but I noticed that with my Maximus AVR USB device, which is based off the at90usb162, when it was flashed properly, the LED (when connected to the PC) lit red. I had tried the AerialX hex and it wouldn't flash correctly.
Used an earlier hex and it worked no problems. When I did manage to flash the USB device, Windows 7 popped up with USB Hub detected.
Hope this helps.
Oh and like cSharpShooter stated, try the power thing. I noticed that I have to switch off my console for the JB to work. Though the LED should always be lit.
Mine works fine (Maximus AVR here), but the hex I am using the LED's don't work.. just make sure you have the right firmware. Also make sure all USB (other than the AT90USB) is unplugged when you do the initial startup.
This most likely will be that you are using the wrong hex or a not working one, try flashing it again with a correct one that is for your board and follow the usual procedures. Also make sure you have 3.41 if not then it won't work.
I've done some of the work for you by finding the correct hex that is working and is up to date with hermes payload so you'll be able to use Backup Manager v2.