Hi,
It would be helpful for us to know the exact Make/Model of the computer you are having this problem with.
Given we have to wait for that, a general guess as to your problem was that if you performed a Win8.1 upgrade on your computer from an earlier version of Windows, say XP/VISTA/WIN7/WIN8, and your 2nd hdd was plugged in, this would account for your problem. We see this frequently on the forums with self-upgraders.
It's NEVER a good idea to upgrade a PC to a newer version of Windows with any additional hdd's plugged in the Motherboard or via USB or Firewire, or eSATA ports, or any other external devices such as printers, webcams, etc. Most Home Users are not aware of this very important consideration; as they are not...