After compiling my LaTeX document to PDF, I noticed that its internal bookmarks were using an incorrect hierarchy. Compare the bookmarks tree to the table of contents below:
How can this happen and how do I fix it? I never tinkered with the bookmarks system manually.
Here's a Minimal Working Example:
\documentclass[a4paper,oneside]{report}
\usepackage[a4paper]{geometry}
\usepackage[dutch,english]{babel}
\usepackage{subfigure}
\usepackage{graphicx}
\usepackage{lscape}
\usepackage[font={it,sf},labelfont=bf]{caption}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage[colorlinks=true,linkcolor=black,citecolor=red,urlcolor=red]{hyperref}
\title{AAA}
\author{AAA}
\date{AAA}
\begin{document}
\maketitle
\null
\vfill
\thispagestyle{empty}
\abstract
\chapter*{Introduction}
\addtolength{\parskip}{10px}
\setlength{\parindent}{0cm}
\pagenumbering{roman}
\newpage
\selectlanguage{english}
\addtolength{\parskip}{-10px}
\tableofcontents
\addtolength{\parskip}{10px}
\chapter{A}
\pagenumbering{arabic}
\section{AA}
\subsection{AAA}
\subsection{AAB}
\section{AB}
\section{AC}
\subsection{ACA}
\subsection{ACB}
\section{AD}
\newpage
\section{AE}
\chapter{B}
\section{BA}
\section{BB}
\subsection{BBA}
\section{BC}
\subsection{BCA}
\section{BD}
\subsection{BDA}
\subsection{BDB}
\subsection{BDC}
\section{BE}
\chapter{C}
\setcounter{chapter}{0}
\renewcommand{\thechapter}{\Alph{chapter}}
\chapter{D}
\selectlanguage{dutch}
\section{DA}
\subsection{DAA}
\subsection{DAB}
\subsection{DAC}
\subsection{DAD}
\subsection{DAE}
\subsection{DAF}
\subsection{DAG}
\newpage
\bibliographystyle{plain}
\end{document}
And here is the file list:
*File List*
report.cls 2007/10/19 v1.4h Standard LaTeX document class
size10.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
geometry.sty 2010/09/12 v5.6 Page Geometry
keyval.sty 1999/03/16 v1.13 key=value parser (DPC)
ifpdf.sty 2011/01/30 v2.3 Provides the ifpdf switch (HO)
ifvtex.sty 2010/03/01 v1.5 Detect VTeX and its facilities (HO)
ifxetex.sty 2010/09/12 v0.6 Provides ifxetex conditional
geometry.cfg
babel.sty 2008/07/08 v3.8m The Babel package
bblopts.cfg 2006/07/31 v1.0 MiKTeX 'babel' configuration
dutch.ldf 2005/03/30 v3.8i Dutch support from the babel system
english.ldf 2005/03/30 v3.3o English support from the babel system
subfigure.sty 2002/07/30 v2.1.4 subfigure package
subfigure.cfg
graphicx.sty 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
graphics.sty 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
trig.sty 1999/03/16 v1.09 sin cos tan (DPC)
graphics.cfg 2007/01/18 v1.5 graphics configuration of teTeX/TeXLive
pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX
infwarerr.sty 2010/04/08 v1.3 Providing info/warning/error messages (HO)
ltxcmds.sty 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)
lscape.sty 2000/10/22 v3.01 Landscape Pages (DPC)
caption.sty 2012/02/19 v3.2f Customizing captions (AR)
caption3.sty 2012/01/12 v1.4b caption3 kernel (AR)
xcolor.sty 2007/01/21 v2.11 LaTeX color extensions (UK)
color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
dvipsnam.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
hyperref.sty 2012/05/13 v6.82q Hypertext links for LaTeX
hobsub-hyperref.sty 2012/04/25 v1.12 Bundle oberdiek, subset hyperref (HO)
hobsub-generic.sty 2012/04/25 v1.12 Bundle oberdiek, subset generic (HO)
hobsub.sty 2012/04/25 v1.12 Construct package bundles (HO)
ifluatex.sty 2010/03/01 v1.3 Provides the ifluatex switch (HO)
intcalc.sty 2007/09/27 v1.1 Expandable calculations with integers (HO)
etexcmds.sty 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
kvsetkeys.sty 2012/04/25 v1.16 Key value parser (HO)
kvdefinekeys.sty 2011/04/07 v1.3 Define keys (HO)
pdftexcmds.sty 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO)
pdfescape.sty 2011/11/25 v1.13 Implements pdfTeX's escape features (HO)
bigintcalc.sty 2012/04/08 v1.3 Expandable calculations on big integers (HO)
bitset.sty 2011/01/30 v1.1 Handle bit-vector datatype (HO)
uniquecounter.sty 2011/01/30 v1.2 Provide unlimited unique counter (HO)
letltxmacro.sty 2010/09/02 v1.4 Let assignment for LaTeX macros (HO)
hopatch.sty 2011/06/24 v1.1 Wrapper for package hooks (HO)
xcolor-patch.sty 2011/01/30 xcolor patch
atveryend.sty 2011/06/30 v1.8 Hooks at the very end of document (HO)
atbegshi.sty 2011/10/05 v1.16 At begin shipout hook (HO)
refcount.sty 2011/10/16 v3.4 Data extraction from label references (HO)
hycolor.sty 2011/01/30 v1.7 Color options for hyperref/bookmark (HO)
kvoptions.sty 2011/06/30 v3.11 Key value format for package options (HO)
pd1enc.def 2012/05/13 v6.82q Hyperref: PDFDocEncoding definition (HO)
hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
url.sty 2006/04/12 ver 3.3 Verb mode for urls, etc.
hpdftex.def 2012/05/13 v6.82q Hyperref driver for pdfTeX
rerunfilecheck.sty 2011/04/15 v1.7 Rerun checks for auxiliary files (HO)
supp-pdf.tex
nameref.sty 2010/04/30 v2.40 Cross-referencing by name of section
gettitlestring.sty 2010/12/03 v1.4 Cleanup title references (HO)
problem.out
problem.out
***********
It appears that these two lines are wreaking havoc:
\setcounter{chapter}{0}
\renewcommand{\thechapter}{\Alph{chapter}}
