This problem might be a combination of two well known issues:
1. iBooks epubs with embedded fonts usually require an unmanifested com.apple.ibooks.display-options.xml file in the META-INF folder with the following content:
Code:
<?xml version="1.0" encoding="UTF-8"?>
<display_options>
<platform name="*">
<option name="specified-fonts">true</option>
</platform>
</display_options>
2. InDesign obfuscates fonts by default, which KindleGen doesn't like.
You may want to add com.apple.ibooks.display-options.xml and replace the obfuscated fonts with unobfuscated ones.