It is the drive from which your system boots. An error message regarding this often means that your computers BIOS cannot find a bootable disc. Check the connectors on your hard drives---a cord might not be properly seated.
If everything appears to be fine cord-wise, try plugging in and unplugging your USB peripherals each time you boot. I know in the past one of my motherboards refused to recognize that I had a hard drive unless I had a specific flash drive plugged in as well.