Yeah it sounds like it could be a flaky hard drive, though usually that shows up when you boot (most newer computers have a system that monitors the health of a hard drive).
Checking the hard drive would be a good step, most manufacturers have software on their sites now that you can download, burn to CD, and boot from and test and format the hard drive, that's what I would probably do at this point. That kind of corruption isn't normal.
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Uncertainty is an uncomfortable position.
But certainty is an absurd one.
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