Unfortunately, I'm seeing a similar issue, if not the same, under Win98 as well.
I set the jumper to ALT, program the i-pac the way I want it, receive a SUCCESS message, and use it as I programmed during that Win98 session. As soon as I reboot, however, the settings are lost on the i-pac.
The way I've gotten around it is to run a batch file in my startup menu that runs the command ipacutil ipacutil.cfg /B. This way, it gets configured every time I launch into Win98. I wish I didn't have to do this, however.