Thanks guys
DiapDealer - I downloaded the latest version of Sigil and looked at the font obfuscation options. Indesign CS6 uses the IDPF method to obfuscate the fonts (Sigil tells me) - when I change it to the Adobe method and resave the file it crashes Sigil when trying to reopen it(!), the fonts still don't work in iBooks (and no longer works in ADE (2.0.6XXX)). I have attached my sample ePUB if you wanted to look at it (the original one from ID).
JSWolf - thanks for the tip, that could be useful.
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