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Chocky: Uninstalling calibre doesn't touch either the libraries or the configuration folder. With the problem you are having, I would try renaming the configuration folder. The next time you start calibre, it will show the setup wizard and create a new configuration. But, as the plugin zip files are magically being restored to a previous version, I would wait for a few minutes and check in case the configuration is being restored by some other process.
Other things I would check:
- Do other configuration changes stick across restarts? You need to change something that is stored at the calibre configuration, not in the library.
- If you uninstall another plugin, does it stay uninstalled?
- If you uninstall the reader plugin, does it disappear from the plugins directory? Does it reappear when you restart calibre?
- Are you sure calibre is actually closing when you think it is? Do you have it in the system tray?
- Are starting calibre directly or do you have a batch file wrapping it?
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