If your computer is scheduling chkdsk on it's own, then either it's flagged a sector on the hard drive, and it needs to "repair" it be moving the data from it, to another sector, and mark the old one bad, or it is having issues removing the flag.
I suggest using Hirens boot cd and perform the non-destructive tests such as HDD Regenerator, the test CAN take a long time on larger drives.
Last but not least, replace the cable between the motherboard and hard drive, a flaky connection or cable can cause intermittent issues, and cause this behavior. It can also cause the drive to appear as "bad" and will cause the system to perform a chkdsk operation at boot.