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She uses InDesign CS6 on her Mac to make the books and saves them to EPUB 2.0
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Very poor workflow choice. CS is not intended to produce good eBooks. Anyway...
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Can anyone give me some pointers on where to look on solving this problem.
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I suggest to first check whether the produced EPUB files are valid, according to the IDPF specs. There is a free validator at
http://code.google.com/p/epubcheck/
Then, try a differential analysis of an EPUB file that works on that device/app and another one that does not work. Check for OPF and NCX structural differences. If even this does not succeed, inspect the XHTML page source code, for "strange" elements (frames? javascript stuff? strange unicode chars?)