Sounds like the thing is either doing a full-scale virus-check of all drives,
a background de-frag(?) or maybe a virus infection.

Needs serious investingation urgently, to play on the safe side.
Try looking in the task-manager/processes list and see if you can see
a process either starting/stopping with the same time-cycle,
or one whose cpu-usage (CPU column) is jumping up and down to the same beat.
Note:: the process starting/stopping or cpu-usage may not exactly match the
HDD activity, but it will be the same timing pattern...

Best of luck.