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I tried to bring down most services, to try to get the disk out of sleep routines, to get it out of indexing of windows, but still no go. I suspect it's low level I/O related but can it be fixed? Or at least workarounded.

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do you want the why or how can it be fixed? Cause the why can be easily answered. Could be one reason – Thomas May 20 '11 at 7:11
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Could be also a bad disk drive sector which makes the hard drive get stuck for a while before finishing the read. Disk read errors usually block the whole system. Make sure to check the disk, just in case.

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Not necessarily true, but may be the case. – j riv Sep 12 '11 at 12:57

Its a little unclear from your question, did you edit the settings in the power control panel, to disable the sleep mode for the HDD? Most laptops will have this enabled for power saving purposes, but the freeze will only happen when starting to use the computer after a period of inactivity.

If the problem still persists, then it is likely to be disk thrashing as Thomas stated in his comment. However, first you should make sure all your drivers etc are up to date for your computer (check the manufacturers website as well as windows update, assuming you are using windows).

In the case of thrashing, you may be able to identify a certain application causing it, using system monitor tools. For Windows, try using Process Explorer, it has many configuration options you can use to show disk IO (number of reads/writes, bytes read/written etc).

Low memory and/or excessive paging could be another cause, can you edit your question to include your computer specs? Processor model, amount of RAM, operating system, and free space left on your system drive (C: on windows) would be useful info.

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Use LatencyMon or DPC Latency Checker to see which driver is having issues. You can read a tutorial on diagnosing problem drivers in this superuser answer.

My feeling is that it's bad sectors on the hard drive. If so, you will see disk errors in the Windows event log.

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