You should be able to regain control by holding down player 1 button 1 and powering on the JPAC.. So, hold down whatever key/button is attached to player one, switch 1, then unplug the USB cable from the JPAC and wait a bit, plug it back in.. Once you do that, in a perfect world, you can then go into the JPac software and it will be recognized and you can program it or do whatever.
Best of Luck,
Zeosstud