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This is what happened:

  1. I attached an external hard disk via USB
  2. Started my Vista machine
  3. It took an unusual long time too boot up with lots of hard disk work
  4. I eventually logged in
  5. Internal system disk heavy duty didn't stop for the next few minutes and system was very unresponsive so I clicked Start > Shutdown
  6. Detached external disk
  7. Started machine up with the same symptoms as previously

I'm 100% sure external disk isn't infected

I also tried turning off Windows Search service after second logon (because I though disk indexing could be going on even though this wouldn't explain the unusual boot time to logon point). Service was still in Starting mode after 10 minutes or so after I logged in. With service turned off, disk utilisation didn't go away. So I turned it back on (after about 5 minutes).

I checked processor utilisation in Process Explorer (sysinternals) but processor was pretty much on 0%. There's plenty of free system memory so pagefile thrashing is out of the question.

And there were no Windows updates, since it's Thursday and machine updated two days earlier already (on regular update Tuesday).

My system disk is less than half full.

What else could be wrong?

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You could Try checking the HDDs with the check disk utility,[on cmd type "chkdsk {drive:} /f" /f checks and fixes error in the volume. you can use /r and try to recover information from bad sectors (takes a lot more time) sometimes this behavior shows when theres a problem with the File system of one of the HDD. hope this helps..

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Could it be your HDD is finding bad sectors on the disk and taking a long time to get over them. I generally can tell with bad sectors by either putting my hand on the HDD and feeling for the "tick, tick, tick" in a rhythmic pattern without the heads being flung around the HDD. Another way is to put a screwdriver against the side of the HDD and put the plastic part up-to your ear so you can listen to what the HDD is doing.

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I haven't error checked my system disk, but I'm 99.9% it doesn't have bad sectors. – Robert Koritnik Nov 19 '09 at 21:01
If you're 99% sure its not bad but you've eliminated everything else you can think of then why not test that 1% of doubt then you'll be sure? – RobM Dec 20 '09 at 19:17

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