Vinbryant,
Hold FX1 and FX3 while powering amp on. Lights should flash then go out. Do not click SAVE button. The lights may stay off, but go ahead and hook up a usb cable to amp and CPU. Open line 6 updater. Updater "should" recognize the amp now. Run firmware V1.00 install. Should be back in business after the install is complete.
**Let me know if the above procedure doesn't work. There is one more trick if updater doesn't recognize the amp.
Thanks,
-DFBF