I'll start off by saying that I'm not asking anyone to start re-scanning the manual. I was just checking to see if my downloaded version is as it should be or not.
I have an original hardcopy, but wanted the soft version to view at work. It would be nice to have a complete set to view, but I might just buy a second copy anyway.
To answer your question, it seemed to be any page/section that I wanted to look at
Specific examples are :
Daily (pre-ride) checks. These are referred to in the Routine section, but I couldn't find them. In the book I believe they are between the Intro and Chapter 1.
Picture problems seem more common - Pages 8 and 19 of Routine are badly affected, as are many of the pictures in the Engine section. I've not really looked through much more yet, but the problem did appear quite frequent.