It seems that there is a bug with embedded fonts in an ePub.
Embedded fonts in an ePub created with InDesign CS6 do not show in iBooks. The "com.apple.ibooks.display-options.xml" file is included.
If I use Sigil to obfuscate the fonts with the IDPF method, the ePub is working in iBooks.
The Test files can get downloaded under the following link: https://dl.dropbox.com/u/9429870/CS6FontEmbedding.zip
(Hopefully there is an update with these lots of bugfixes coming soon)
I've got the same problem with you. I'm stucking with embedded fonts. My epub created with inDesign CS6 cannot open in Sigil if it is one document type. If epub created with book of documents in inDesign, it's OK. Maybe I have to back to CS5.5 in order to open it in Sigil to embed fonts.
Is there a way to embed fonts after exporting epub by inDesign without using Sigil ? I've tried many ways I've Googled but they didn't work.
Need help seriously.