Look at the Look and Feel screen in the conversion tab. I routinely go to filter style information and put check marks in fonts and margins. You can also change the minimum line height on the same screen.
I mentioned the calibre style sheet because I have not had this problem with kepubs or with ePUBS that have either not had their DRM removed or only had the drm removed without making the kind of changes that result in having calibre shtuff in the style sheet.
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