I did some various tests. I was put on track the moment one of my books did work. Since I always use the same core components and I forgot to link my stylesheet, the issue is in my stylesheet.
Since I already found out earlier that iBooks has some issues with height: 100% in the html and/or body and the @page declaration, that was my initial focal point. A test case was easy developed.
The @page is not the issue, the issue is the 'height: 100%' in the body/html class of my stylesheet. Strange part is, that when the file is big enough it will work anyway.
Since the 'height: 100%' is not doing much, I will remove it from my core stylesheet.