Lars,
I don't know what could be going wrong. For me, CustomReader does indeed change the font, text alignment, and paragraph styling of Reader printouts (and saved PDFs), as it's supposed to.
I thought you were trying to change something else in printouts, such as the margin width.
I'm sorry, but I have no suggestion to make it work. Perhaps it's only failing on certain pages (i.e., all the pages you've tried it on)? Please give me one or two URLs of pages where you are certain that CustomReader's styling is not affecting printouts from Reader, and I will try to reproduce the problem.
Chul