Ah ha, should have guessed that... Update: have now completely removed calibre (via the uninstall link), then deleted the database folder and the data folders \application data\calibre and application data\kovidgoyal.net. I then rebooted and reinstalled .4.1.3.1 and you guessed it, same problem (but as I deleted the config files it did ask where to store the library so apparently they weren't the problem).
*sigh* on the bright side, this version runs flawlessly on my xp box.
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