Hi Stephan - There are two reasons I can think of. The first is that your PDF is actually not containing text and instead just contains images of the content. If that is the case, there is nothing that can be done until the book is OCR'd.
If that is not the case, then perhaps I need to adjust the regular expression that finds the ISBN numbers. If you have a PDF example, drop me a PM with a link to somewhere I can download it from.