Problem (manually) tagging document: Tagging one text area tags all text in document

I've been having some trouble getting a inDesign document to tag properly in InDesign CS5.
The document has several different blocks of text, and I can see that they are each separate in the layer panel, and that they are not locked or grouped.
Yet, when I try tagging the document, it is treated as though all the text is in one element and the entire text of the document is tagged together.
The only element that seems to be able to be tagged separately is some text in the header, but it is not relevant for the XML I plan to export.
Any tips on getting this to work? I suspect the original file might have been created in a different version of InDesign, maybe that has some affect?

It sounds like you applied a tag to a portion of text in the flow of threaded frames, and all of the text within the threaded frames is now applied the story tag. This is normal and if you need to, you can create additional tags and apply within the story.

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