Ok, I think I found the problem, but I'm not sure.
Both ground wires I have going from the IPAC go to the buttons, but they are tiny loops.. each ground wire only touches 2 buttons. The rest of the buttons are all linked via another black ground wire to a small switch that can toggle left and right (I'll post a pic tomorrow). Right after the wire connects to a corner of this switch (appears soldered on) it goes into a small (5 in wide, .5 in height) black box of wires. The wire that matches coming out the other end of this is going into the IPAC under the SW1 slot.
So, my ground wires aren't really connected to the rest of the buttons, and I don't know why these buttons are all linked to this mystery switch and the SW1 slot. I bought this machine and it worked fine for a long time. Any idea what I should do next?