Thanks for that. That was interesting to hear. What you're describing does sound like it could be part of the same thing I am seeing. Maybe the better solution would be for me to go ahead (or go back) and create a longer TOC with a 1:1 TOC entry/xhtml file correlation.
That way, even if it does mean that the TOC would include things that I would deem unnecessary, at least I can determine how they appear there rather than have some automated system pluck out pieces of code (it seems to choose the names of the itemrefs from the spine in the content.opf) and put them on show in the TOC.
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