I've PMed you the log, I hope it's helpful.
The only peculiarity of my setup (which was not a problem up to now), is that I'm using a 3-column setup for my annotations:
- Column A: Annotations added by me manually, inside Calibre
- Column B: Annotations used by the GUI Annotations plugin, not touched by me at all
- Column C: The result of A + B, used to export my annotations to an ebook by Calibre's "Export Catalog" feature.
The above setup has been working without issues, I don't know what might have changed and at what point.