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It does not have anything to do with plugins. Of course I cannot be sure of that, but given that calibre-parallel.exe is being flagged, ti is almost certainly because calibre-parallel.exe is used to download metadata and news sources which means it often contacts servers online. I'm guessing that using it ins some ways, but not others, triggers whatever heuristics AVG uses to detect trojans.
And I'm sorry but I dont see anything I can do to fix that in calibre. Since AVG does not tell you why it thinks calibre-parallel.exe is a threat, and moreover whether it thinks it is a threat or not varies from time to time, release to release, AVG version to AVG version, trying to fix that in calibre is a mugs game.
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