This is the best answer I could find.

http://www.tomshardware.com/forum/53192-63-what-make-computer-check-disc-startup

When it runs the chkdsk does it report finding and correcting any errors ? -- If it does then it could be a HDD problem ( If it is finding bad spots in the magnetic layer of the disk and having to redirect pieces of the files and mark those bad spots as bad sectors so they no longer get used ) - an occasional problem or bad sector is not really anything to worry about but if it starts to become more prevalent then you might want to consider replacing the HDD or at least making a backup of any important files just in case. 

If it didn't find any problems and is working fine now I'd figure it was just some interruption that occurred while shutting down (possibly a software program update that didn't clean up properly after it ran) and for safety the system ran the check and wouldn't worry about it unless it reoccurs.