After looking at this more, I believe the problem is with gscan2pdf. Its page numbering suggests that it received pages, but they just don't show up. For instance, if I scan a single page in duplex mode into an empty document, if gscan2pdf is going to miss a page, the resulting page may be numbered either 1 or 2. If I scan two pages in duplex mode, after the first sheet is processed, the second sheet will start at page 3 in the scan progress box, even if one of the sides of the first sheet haven't appeared.
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