We have just solved an interesting query in which an unformatted document was not formatting Endnote references correctly, was duplicating tables and producing error messages such as “Not a valid bookmark self-reference”. This seems to be connected to the document containing other dynamic links to tables and figures. Endnote was trying to convert all these links into citations. The solution was to break the links to the tables and figures by going to Edit, Links, highlight all the links and click Break link. Reformatting then works perfectly.
This means that if you want to use dynamic links to data, you should leave formatting your references as the very last thing before publishing your work (ie disable instant formatting), so that you can convert the other links into static links first.