I assume that your assumption is correct. If you have multiple internal hard disks it may require an additional selection. Is the Hard Drive listed and identified properly in the system bios? Have you done anything else in the bios that may have changed the mode that the hard disk controller operates at? Have you changed it from AHCI to Native IDE or Compatability Mode? If so you will probably need to return it to it's proper setting.
And when you did the backup after being prompted, did the prompt include any warning regarding any pending hard drive problems / failure?