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Did you try the -ppgs option? This post-processes with Ghostscript and sometimes helps with problems like this. The issue is that k2pdfopt is taking the original PDF and adding cropping commands to show cropped portions of each page (it does this in “native” mode), and it sounds like some software doesn’t respect that or ignores that. You could turn off native mode also (-n-) but that will bitmap each page and may not be what you want.
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