This message generally only pops up during boot. If it popped up while the OS was running I would wager either the computer crashed and rebooted and this popped up or malware was simulating the message. This message pops up during boot for one of a few reasons.
- BIOS could not detect your hard drive
- Hard drive is beginning to fail
- A partition was marked active that shouldn't of been
- Your MBR is corrupt
Most likely the hard drive is beginning a spirally decent to failure. I would suggest running a DFT test on the harddrive, seatools work really well and are available as a stand alone or as part of the Hiren Boot Disc. You could also verify whether or not the computer crashed. There should be a dump file in C:\Windows\Minidump if it did.