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What error message are you getting? "Permission denied" on some executable, Calibre can no longer read it's data directory, what?
You can see a log of what software has been installed and what updates were made in Synaptic. Just use File->History. So if you can recall when Calibre last worked, you can look at what's been installed/updated since then and maybe get a clue.
I'm thinking this is more likely a user or script oopsie that got a little too sloppy with the chmod or chown command. But first you have to better describe what you're seeing (specifically) before we can speculate further.
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