Windows

Windows runs Scandisk at startup when it detects disk errors.

Are you letting scandisk run, or exiting?

If you do not run scandisk, and fix all errors, it will continue to run at startup.

Run scandisk for all drives from Windows.
Either check the box to repair errors, or correct any errors manually.

This should take care of the problem.

You can also install tweakui from Microsoft. One of the options is to set the behavior of scandisk at startup.

I had an ongoing scan disk situation when the hard disk was set to a different set of parameters in the bios than what it was originally formated under.

start-run-msconfig

I know there's an option for scan disc somwhere in msconfig (not at a 9x box right now) anyways, you can set (or unset) it to run scandisc each time