Sounds like a failing hard drive. Symptoms just happened to coincide with the Calibre update. The thing to do when something like the above happens is to pull the HDD from the system, slave it and create an image/backup while it's still possible to read from the drive. You certainly don't try to keep writing to it.
I have an Intel Atom 330-based PC (slower than later P4s) that handles a Calibre library with 3,000 titles just fine with Microsoft Security Essentials running in the background so I doubt Calibre is the culprit. It's possible that the Calibre update (and resulting metadata.db upgrade) brought the issue to the forefront but I reckon it would still have happened sooner or later.
Quote:
The hard drive in your computer is in one of two states right now. It's either going to fail or it already failed.
-Chris Pirillo
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