Do you know when this last worked?
Can you install some older releases (e.g. from the debian archive or from sourceforge[1]) and give me an idea when this last worked.
I should also note that gscan2pdf does not distinguish between paper sizes that were default and those which were defined by the user, so I suspect the problem is caused by changing to a smaller paper size. Can you have a play and see if you can confirm this?
If this is problem only started recently, but you can't find a gscan2pdf version where it worked in the past, then it might be that a change in the backend is triggering a bug that has always been in gscan2pdf.
[1] https://sourceforge.net/projects/gscan2pdf/files/gscan2pdf/
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