Sometimes Windows will run a virus scan on boot if you've got a program that does it, like avast.
The consistency check doesn't have anything to do with viruses or malware though. It usually means some change didn't get made correctly on the drive (power outage or a system crash resulting in the drive getting turned off while it's in the middle of doing something is a common cause) and the file system doesn't like the state it's in. Windows fixes it by itself and it's usually not a problem. You can force it by typing chkdsk /f in command prompt.
Another reason why I like having a Mac.
Macs do the same thing, the command to do it is fsck -fy and you can read the documentation
here.