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I think what he's trying to say is that you should do a test case conversion in the GUI for the purpose of figuring out which arguments the GUI uses. There may be issues with the arguments you pass to ebook-convert, for example, I could see the margin=0- arguments fighting with the preserve-aspect-ratio argument and winning. If you converted via the GUI as a test, you'd be able to see, for example, if the margin arguments still get passed when you select to preserve aspect ratio.
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