Adding the following com.apple.ibooks.display-options.xml file:
Code:
<?xml version="1.0" encoding="UTF-8"?>
<display_options>
<platform name="*">
<option name="specified-fonts">true</option>
</platform>
</display_options>
in the META-INF folder appears to fix this problem, so this is probably a curious quirk behavior designed to avoid some problem that the iBooks folks saw with old, broken eBooks.
I would strongly suggest just adding the file. It will save you lots of problems and head scratching.