To test the ground, I just touched the wire for the player 2 start button to those switches and it worked. Then I tried the 6 button from player 1 just in case it mattered that it went through the jpac and it worked two. So I didn't think it could possibly be the ground or the switches.
I tried the software and that seems to have worked. I don't understand because I thought that the default couldn't be lost, but it works now, so all is well.