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The encryption is probably the Font Mangling. Is there any chance to use a newer version of InDesign, because the font problem is just one of many issues with ID CS4 that made it a 'joy' for everyone to use (export and then fix up all the problems by hand).
If you can't get a newer version of InDesign (if it is just a short term thing, then you can download a 30day trial from Adobe...), I would strongly suggest looking into using a different program to do the conversion, such as Calibre for just conversion if you already have it in a good eBook format already (I've also heard decent things about using Atlantis to convert from Word docs, but I haven't tried it myself), or Sigil to help you create the file
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