I thought of a couple of other things to try. They might help work out when the corruption happens.
Firstly, connect to the PC without calibre running. Then use a SQLite tool to do the database check. I use a Firefox plugin called "SQLite Manager", but there are native applications for all OSes.
A little harder would be installing SQLite on the device and then running the check while it is running. There already is an SQLite library, but I don't think there is a command line tool to run it. I know I have seen mention of it in the developers section, but haven't followed it up. After that, telnet could be enabled and used to run it. For this, I am thinking that checking after the processing is finished and before connecting to the PC might help to work out when the corruption happens.
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