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I've got a feeling this has something to do with the EPUB file containing multiple XHTML files, and the same "id" value being used in more than one XHTML file. When compiled into a MOBI file, the content is rolled up into a single file, but I've got a notion the "id" values used in links like these ones in your NCX file remain unchanged. So if you have a "section1" bookmark in both "chap01.xhtml" and "chap02.xhtml", when converting to MOBI using MobiPocket Creator, I think you end up with the problem of multiple occurrences of the same bookmark name.
If I'm right, and this is what is causing the problem, you need to go through the EPUB and change these bookmark names so that they are unique without relying on being in different files (so the example given might become "chap01sect1"), and change all references that point to each bookmark (such as references in the NCX file, OPF file and inline TOC).
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