I can't answer for sure, but most of the issues I had in these kind of cases were coming from bad fonts. Shitty fonts from hell. As far as I know, Scribus despite some nasty bugs while editing, generates among the best PDF files possible, compared to other products. But if one font is bad, beware... Try to get a list of fonts used by your publication and have a look at the fonts issue in Scribus help pages...
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