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It would be a lot easier to work out what your problems are if you create some sample documents that show the issues you're having.
One thing I did forget to mention is that InDesign CS5 has a known bug with internal links when 'Include InDesign ToC Entries' is ticked, as it fails to include the correct filename along with the name of the anchor. If your book uses a lot of links in the text (e.g. for footnotes or an index), then it's a better idea to export without the InDesign-generated ncx ToC and edit the output with either Sigil (convert paragraphs with the relevant heading styles to <h1> etc tags) or Calibre (use epub-to-epub conversion and insert an XPath expression that will pick up the styles used in your chapter headings).
But if the only hyperlinks are on the ToC page then it's easy to edit that manually and enter the required filenames to go with the anchors.
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