Ok here's my problem. My primary SATA drive's boot loader started acting funny. After messing around a bit I re-wrote the MBR. At this point, the boot loader wouldn't load the OS (and damn me for not writing down the error message, something about not finding /dev/root I think if that makes any sense). I finally conceded and rebuilt the system from scratch. Now the BIOS isn't detecting the primary drive that's been rebuilt, however, I can use it normally if I use a rescue CD like "SystemRescueCD" and tell it to boot from that disk. This seems very strange to me that the BIOS doesn't see the drive at startup, yet post bootup it's available. Maybe someone could shed some light.
Linux will ignore what the BIOS says and identify the hardware directly.
As to why the BIOS isn't detecting the drive (which is obviously there), I think you'll have to post some hardware details, it would also be worth running the manufacturers drive test tool (or Ultimate Boot CD).