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With conversions you should experiment with settings on one book/comic rather than bulk. When you have a satisfactory output for one book/comic you can change the settings in preferences. But even then some books/comics may need specific settings.
Did you try checking the Landscape setting in Comic Input settings ?
The setting in Conversion->Output profile will also effect results - if you have it set Kobo then as an experiment try setting it to Generic.
BR
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