I almost always get that problem with Win98 installations -- and I usually install Win98 directly from CDROM.
To correct this, install the Via 4-in-1 drivers, which will give you a working "IRQ Holder for PCI Steering". I usually uncheck everything else in the 4-in-1 bundle, but make sure to get the IRQ Holder installed. I personally don't use the Via-optimized ATAPI drivers that come in the 4-in-1 bundle, as I've had a few horrible experiences in the past.
Anyways, once you have PCI steering working properly, you can re-enable the "IRQ for VGA" and "IRQ for USB" options in the BIOS without negatively impacting the Win98 system.