Constant hd and cpu activity, slow computer

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Hoping someone can help me here before I go and have to re-install Windows.

This started last night while I was playing Deus Ex. All the sudden I started lagging out and freezing, so I saved the game and went to see what was going on with the computer.

The hd is going constantly, the light is on constantly and the drive is constantly reading/writing something, the sound alone is driving me nuts, but when this happens the computer becomes almost non-responsive. It took about 6 tries to get task manager to open, I'm unable to open or close a page or do anything. Sometimes I can do stuff but it's extrememly slow, like it'll take 30 seconds for a page to open and then it's super slow.


This morning it was fine, then it started again about 30 minutes ago and is still going. I see no windows updates running, no antivirus, no backup, nothing.

When this is happening I'm showing 10-40% cpu usage and about 3gb of ram usage, yet under processes I see nothing using cpu at all. I have updated and ran Malwarebytes and MSE last night and found nothing. I did a disk cleanup and defrag about 3 days ago as I regularly do.

Right now while I'm typing this with only Firefox running I'm showing 40% cpu usage. The ram fluctuates between 1.5 and 3.5gb of ram usage, and the hd is going nuts constantly doing something.

What is causing my hd to go nuts, high cpu usage and slow my computer to a crawl? I'm stumped.
 
One more thing: I believe Vista (and Win 7) perform some automatic defragmenting in the background once in a while. I usually prefer to turn that off and do the defrags myself. If that is enabled, it could kick in at random times and slow down your HDD.
Last thought: now the HDD should be "clean", the bad sectors marked out; but if some system files were on these sectors and corrupted, they might need reinstalling. You could run the SFC /scannow as mentioned above (in that case, if something is wrong, it will ask for the OS disk to get the original clean files), or you could just perform a repair-install; you will not lose the programs, but I guess the updates will be gone. Let us know.
 

Yes, that one (planning or scheduling, something like that- I haven't used Vista in a while).
 
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