I had a lot of trouble with two different PCI controllers until I reflashed the BIOS (see thread FIX! - For using PCI...) with the newer OEM version.
But if you are determined to stick with the old BIOS (which you may need to until you can boot!), I did get the cards to boot eventually and they worked fine in DOS and Windows 9x but did not work properly in Win2k. To get them to boot I disabled the onboard Primary IDE, and went into PNP configuration and changed the PNP OS to No, changed the PNP configuration to manual, and restricted all the IRQs over 8 to legacy ISA only. Someone elesewhere on here said there was a problem using high IRQs. It worked for me, although I can't say why.