Ohh, I hate that feeling when you think everything is done....then something comes up and ruins it all.

I'd start simple, it could easily be that the switch is bad. Try connecting a different switch to the 2nd player right. Hopefully that switch will work fine, and you will know you just need to fix or replace the dud switch on your joystick.
If it does turn out to be the ipac4, then i am guessing you have at least a couple unused slots....maybe you could just wire the joystick right control to something like player 4, button 8...and then remap your emulators to the new control.