This is an odd one. It seems there's a known issue with win9x dealing with the Texas Instruments 1410 controller chip the GCT uses. Something about not enumerating the ID numbers properly. There's supposedly a hotfix for it. But it's one of those 'call MS, pay for the privilege, and hope they rebate the fee' sort of things. A huge amount of searching also suggested disabling the ACPI bios and falling back to the PNP failsafe variety. This actually works. Of course I'm sure the abilities afforded by ACPI are screwed up in the process.
I've found what's supposedly a combo patch of win98se service pack fixes. Which may also fix the cardbus problem and allow use of ACPI.
So if anyone else needs to get the mini-PCI slot working it may help to use the PNP Bios instead. Add it using new hardware control panel as a System device. Then, before rebooting, remove the ACPI bios and THEN reboot. It may take a try or two as well as a safe mode trip. You'll lose the video driver in the process so be ready to reinstall it.