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This is certainly a puzzling problem. I don't think the system tray error is a fatal one. Though I am not 100% sure I doubt this has anything to do with the problem. I am running an up to date Sabayon 64 bit with KDE and 2.2.9 and all works flawlessly. My next suggestion is probably clutching at straws, but perhaps worth a try. Calibre configuration settings are usually in ~/.config/calibre, which of course survive updates, downgrades etc. It may be worth trying to run a fresh download of Calibre without these settings. Either run as a different user or move the calibre directory from .config to a safe temporary location. Then run Calibre which will take you through setup. Don't connect to your existing library. Instead let Calibre create a new empty library in a different location. Then see if you are able to add any books from the GUI. You can of course restore your old settings by deleting the new calibre directory from .config and replacing with your old settings.
Two other questions? Are you aware of any changes to your system shortly before the problem occurred? And is your Calibre library stored locally or on an NAS or in the cloud?
Finally, if you are desparate enough and all else fails try running the Windows version of Calibre under Wine or Crossover. Good luck.
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