>Ingar, my lyx file is attached... FN A small lyx file would have been better. I removed the pictures from the first 100 pages of your book and cut the rest of the book. When I compiled it through pdfTeX I did not observe the problem you describe (tried both acroread and kpdf). However, I see you use \microtype. I have had big problems using that command with some publishers. (the glyphs were up and down 1/2 line, randomly) I never observed it on linux, but the publishers mac made a right mess of it.
So try removing \microtype and see if that helps, if not I need a small (less than 10 pages) lyx sample and a corresponding pdf file where the errors are pointed out in text. Ingar
