I have discovered what causes this problem with MOBI output from news feeds. If there is a DIV tag with an empty string for an id, i.e.
Code:
<DIV id=""> ... </DIV>
in a downloaded article, the Calibre code responsible for setting bookmarks for the TOC decides to use that DIV, instead of the begining of the displayed content of the article.
The workaround is to use preprocess_html to find DIVs with id="" and delete the id attribute.
I have been unable to figure out where in the Calibre code this is happening and unfortunately, I'm giving up on this. I've looked in all of the obvious places, and short of exhaustively going through every single source file in Calibre I don't see any way for me to track it down. Perhaps someone who is familiar with the deep-down internals can take this cause and find the error in the code.