McGrath, when you enter the BIOS and enter your "Standard Setup" where you view the disk details, you should be able to change some settings. One of the options for each disk is usually to configure it manually or have it detected automatically on start up. "Auto" settings provide a bit of a "safety net" as if you did change your physical set up (I mean the cables and jumpers to/on your hard disks) the system will detect the changes.

With a working system, my own preference is to use manual settings (having let the system tell me what the disks are) as it gives a slightly faster startup.