If it came from the OS, it’s not likely malware. Win7/8 has disk management utilities built-in that monitor the BIOS SMART system for updates. If the SMART system alerted during the POST (Power On Self Test), Win7/8 is alerting to a fault.
Scanning for malware/spyware is likely to make the problem worse. It doesn’t make sense to scan a failing hard drive. If the fault is with bad sectors or a rotary motor failure, you’ll likely kill the HDD during the scan, ruining the ability to recover the data.
If it’s a pop-up in a web browser, that’s a different story, but the poster says that this is a Win7/8 alert, likely in the system tray. That’s a legitimate system fault.
Running AV is about the last thing I do when looking for Malware. Establishing a baseline and understanding what is running (and what shouldn't be) is priority. Scanning a failing drive would be foolish, I agree.