When exporting GEDCOM some stories, notes and ToDos are not included in the export file. I THINK the problem ones are those that have links to more than one person and not exporting at all rather than exporting twice as you might expect.
At one stage I thought the problem stories were ones that had a photo attached in Family Search (and perhaps a photo link in Rootfinder although not sure about that), but they tend to also be ones that have links to more than one person.
Can dig further it if helps, but checking the export process for notes and stories linked to more than one person might give enough clues.