Old post, but here goes:
Chkdsk trying to run at every boot generally means one of two things: Either the disk has bad sectors, and it wants to run a thorough scan to attempt repairs, or (more commonly), the dirty bit has been toggled via something like pending updates running when the system was shut down improperly.
Run this command from administrator Command Prompt:
fsutil dirty query C:
If it returns this message "Volume C: is dirty", then run this command from the same admin command prompt:
fsutil dirty set C: