Hi,
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)
Kind regards
Yves