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When you set up the sts file, you have an option of for designating which paragraph styles are supposed to break up the publication like this:

Have you assigned any header paragraphs for that?
Initially I believe your issue is one about the naming of the framemaker files. Are you using very long names for the framemaker files or do they include odd characters like / or \ or ? or... something else? Naming may also be an issue with the folders containing the framemaker files.
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