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I'm not sure though whether this is showing me an actual problem, or if it's a specious warning.
It's a warning. Sections may overlap in a file.
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Should this message perhaps only be considered for sections with non-zero size?
Yes. Ignore this message for sections with zero size.
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I'd paste the section headers window here, but there seems to be no copy facility.
Sorry about that. Will add this option within a week or so.