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Well, that is odd, because when using the command-line the default settings from the GUI aren't considered.
And the code should be the same on both platforms (with the exception of certain distros that modify the calibre sources before compiling and redistributing).
But if you installed the binary build like you said, then that shouldn't be a problem.
So apparently the official Windows build and the official Linux build are producing different results on the same input. Which shouldn't happen.
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