Not sure if this has been brought to your attention yet, but it appears that Apple has 'upgraded' the PDF rendering engine in iBooks and it is no longer able to fully render the Coriolis PDF. The affect is present not only in IOS but also MacOS.
The problem has something to do with rendering of art resources. Normally a missing picture wouldn't be a major issue, but sometime the missing art is the page's background image. When this occurs it presents the user with black text on a black background. This makes much of chapter 8 unreadable.
The problem is also present in the Atlas of the Third Horizon.
I'm not sure if Apple will be fixing iBooks any time soon, so you may want to push out a new copy of the pdf that accounts for the new rendering engine.
Reviewer on drivethrough RPG have noticed this and are commenting.
Note: the iBooks PDF rendering engine is also used in a number of third party PDF readers, so the bug is not limited solely to iBooks.