If your IPAC is fairly new then I think you might NOT have any jumpers to deal with.
I dont clearly understand the problem you are having but here is a link to a thread where I was having IPAC problems.
http://forum.arcadecontrols.com/index.php?topic=41941.0As it turned out I just needed to read the FAQ/troubleshooting section of the ultimarc website.
When your having problems with your encoder its usually toward the end of your project and you're probably starting to get excited to start playing games. Its a really frustrating time to start having problems. I know that I wasted a lot of time trying stuff by myself before I asked for help. Then I was told to spend 2 minutes reading the Ultimarc website and my problem was quickly solved.
If you're still having problems, try and post as much detailed info about your problem , your setup and what you've tried so far. It will be easier for others to diagnose your problems.
Good luck.