It seems I have a problem with the headers using the book class. On every chapter when the text is too long the chapter text and the section text merge. Also I don't know how I could make them lower case instead of upper case.
The packages I use can be seen below:
\documentclass[12pt,oneside]{book}
\usepackage[english]{babel}
\usepackage{graphicx}
\usepackage{natbib}
\usepackage{appendix}
\usepackage{microtype}
\usepackage[utf8]{inputenc}
\usepackage[english]{isodate}
\usepackage[parfill]{parskip}
\usepackage[colorlinks,pagebackref,pdfpagelabels=true,plainpages=false]{hyperref}
\usepackage{fancyhdr}
\usepackage{makecell}
\usepackage{amsthm}
\usepackage{pdflscape}
\usepackage{multirow}
\usepackage{mdwlist}
I then include each chapter like this:
\begin{document}
\input{title.tex}
\tableofcontents
\input{overview/overview.tex}
\input{background/background.tex}
\input{chapter1/chapter1.tex}
\end{document}
Here is a bit of code from background:
\chapter{Introduction to Simulation}\label{part:background}
\section{A Simple Example}\label{sec:sim_example1}
There is of course content in between. First page of the chapter seems fine however second page of the chapter produces the text below but mangled. It looks a lot better below.
2.1. A SIMPLE EXAMPLEPART 2. INTRODUCTION TO SIMULATION
\chapter,\section, etc. to provide a short version used for the table of contents and the headers. – Martin Scharrer♦ Sep 27 '11 at 9:47