Sorry, I'm not sure I understand the question. When I start the PC I am always given the "reminder" capability to press F2 (Setup) or F12 (Boot Menu). I have gone into Setup previously where I turned the Primary 1 to Auto from OFF. The next time I went in it showed Primary 1 as and IDE CD-ROM which is what I have connected to the second connector of the boot HDD cable.
I've now turned the Primary 1 back to OFF. When I started the PC again the New Hardware Found message came up so I entered the Wizard and attempted to reinstall the PCA card's included mini driver CD. The did not complete this time, unlike when I originally booted the PC following the PCI card and HDD. It did complete then. NOTE: now the Device Manager displays a new "? Other devices" and sublisting of "? SCSI Controller in yellow question marks. However the former "SCSI and RAID controller" listing is still present and lists "VIA VT6421 RAID controller" as the sublisting, still indicating working properly.
Within the Setup/System Bios the only selection I find that indicates PCI is under the listing "PCI IRQ Assignments." Within this menu I see the listings of ATI Technologies VGA Adapter (IRQ 11), Numerous Intel Corp listings (Serial Bus-IRQ 11, multimedia-IRQ 11, and a number of USB adapters-IRQ's 9, 10, and 11, Network card-IRQ 11), and "unknown manufacturer RAID Adapter-IRQ 10." I have also tried IRQ 9 and 11 also which made no difference.
After reading your message I returned the Primary 1 setup to OFF from the Auto setting I had changed it to when the new HDD didn't work originally. When I turned it OFF, it was displaying "IDE CD-ROM," which is what I have connected to the 2nd connector on the cable with my primary HDD boot drive. But the 2nd CD-ROM drive was working before I changed the Primary 1 setting to Auto and is still working after turning off.
When I turned the Primary 1 to OFF, the next start did indicated New Hardware Found, again. So, I attempted to reinstall the PCI card's included mini CD drivers again. This time, however, it didn't complete as it had following the card's original install and boot up. The driver wizard, despite opening and scanning through all the files on the mini driver CD, repeatedly indicated "cannot find the necessary software." And, as mentioned above, the Device Manager now shows two SCSI listings.
Last, while none of this may be helping or of any benefit to diagnosing my issue, after turning the Primary 1 setting back to OFF, when I started the PC again, I did see new LSI Logic information on the initial black boot screens that initially indicated "Found new hardware" but eventually indicated "No supported devices found," and the startup then proceeded to the Windows menus. The IDE CD-ROM that is connected to the 2nd connector on the primary HDD cable is made by LG and I think it may be what caused the LSI Logic message.
Still at a loss, any ideas?