there are some updates to Windows that deliberate scan the hard drive. it may be the Disk Cleanup wizard. go to the Downloads area on cnet and look for a program called Startup Cop. run it and start disabling programs until you know which one is causing the problem.
Herb....
I am having a problem on my Win 98se box with windows EXPLORER,
( The File / program manager, not IE).
I first noticed the problem a couple of months ago after I DL'ed some updates from uncle Bill's website.
The problem was very intermittent and days would go by without it popping up. For the last two days it has been doing it constantly and I am at a loss on how to figure out was is causing it.
The problem is that when 98 boots up there is continuous hard disk activity after the desktop finishes loading.
Something is scanning / indexing my HD. If I let it go it will eventually work it way through all my partitions and drives and end up at my floppy drive.
I have scan my system with numerous virus checkers. spyware apps, and the like to no avail.
When this is happing if I hit CTR,. ALT, DEL , and open up the close program window the HARD DISK activity will stop. When I hit cancel to close the window the HD scanning will resume.
It will do it when I boot up into safe mode.
It will do it on a clean boot, No Autoexec,bat, config.sys, win,ini etc.
It will continue to run even after I have terminated all apps except windows Explorer.
No other apps are running in the background. MS office indexing has been disabled years ago.
When I open up ATM, (Another Task Manager) I can terminate all Processes except for Windows Explorer and the indexing will continue.
Now when this is happing there will be 4 or 5 threads running under Explorer.exe .
One of these threads will show a tremendous amount of activity .
CPU Usage jumping from around 20% to 90%.
If I just kill that thread everything will work just fine until I reboot and it it starts all over again.
B4 a quick log off or reboot would stop this and it would not reappear for days. Now it happening on almost every boot.
Evidently something is hooking itself to explorer and causing this but I am unable to determine what exactly.
Any one have any Ideas??

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic