PDF Bookmark Hierarchy is wrong

Question

I am having trouble with bookmarks. The hierarchy is not correct. It is giving me something like below. How can I get it corrected?

Acknowledgement
Chapter 1
    Chapter 2
    Chapter 3
Chapter 4
References
Appendix 1

Just to explain a bit more. I am using a style .cls file for my dissertation. In the style file the package are loaded in the following order:

\RequirePackage{amsmath,amsthm,amssymb}     % AMS math, AMS theorem, AMS fonts
\RequirePackage{array}
\RequirePackage{setspace}                   % line spacing
\RequirePackage[vcentering,dvips,a4paper]{geometry} % help with margins
\RequirePackage{color}
\RequirePackage[round]{natbib}                     % this package allows you to link your references
\RequirePackage[dvips,plainpages=false,pdfpagelabels=true,breaklinks=true]{hyperref} % for pdf bookmarks
\RequirePackage[anythingbreaks]{breakurl}
\RequirePackage[all]{hypcap}
\RequirePackage{breakcites}
\RequirePackage{nomencl}

In my main .tex file the packages are loaded in the following order:

\usepackage{float}                      % figure floats
\usepackage{graphicx}                   % graphics package
\graphicspath{ {figures/}{figures/eps/}{figures/pdf/} }% specify the path where figures are located
\usepackage{ifpdf}
\ifpdf
  \usepackage{epstopdf}       % converts eps files to pdf
\fi
\usepackage{ifthen}
\usepackage{fancyhdr}                   % fancy headers and footers
\usepackage{url}                        % nicely format url breaks
\usepackage[inactive]{srcltx}           % necessary to use forward and inverse searching in DVI
\usepackage{relsize}                    % font sizing hierarchy
\usepackage{booktabs}                   % professional looking tables
\usepackage[labelfont={bf}]{caption,subfig} % nice sub figures
\usepackage{mathrsfs}                   % additional math scripts
\usepackage[Bjarne]{fncychap}   % creats fancier chapter titles

Then comes the rest of the main .tex document which imports the chapters of the dissertation:

\begin{document}
    \pagenumbering{alph} % this is needed to clear certain issues with the hyperref package
    %
    %\makeApprovalPage % make the approval page - this is the page that needs to be signed & returned to the thesis/dissertation consultant
    %\makeETDApprovalPage % make the Electronic Thesis & Dissertation page - this page is kept with the electronic copy
    %
    \addToPDFBookmarks{0}{Front Matter}{rootNode} % create a root node named "Front Matter" in the pdf bookmarks
    \addToPDFBookmarks{1}{Title}{a} % add a pdf bookmark to the title page
    \makeTitlePage % make the title page. Make sure you properly set the \docType
    %
    \pagenumbering{roman}
    \setcounter{page}{2}
    %
    \makeCopyrightPage % make the copyright page
    %
    \addToPDFBookmarks{1}{Dedication}{b} % add a pdf bookmark to the dedication page
    \include{front-matter/dedication} % include the dedication
    %
    \addToPDFBookmarks{1}{Acknowledgements}{c} % add a pdf bookmark to the acknowledgements page
    \include{front-matter/acknowledgements} % include the acknowledgements
    %
    \addToPDFBookmarks{1}{Quote}{d} % add a pdf bookmark to the quotation page
    \include{front-matter/quote} % include a quote
    %
    \addToPDFBookmarks{1}{Abstract}{e} % add a pdf bookmark to the abstract page
    \include{front-matter/abstract} % your abstract
    %
    \addToPDFBookmarks{0}{Table of Contents}{f}
    \tableofcontents % generate a table of contents
    %
    \addToTOC{List of Tables} % this will add the list of tables to the Table of Contents (TOC)
    \listoftables % generate a list of tables
    %
    \addToTOC{List of Figures} % this will add the list of figures to the Table of Contents (TOC)
    \listoffigures % generate a list of figures
    %
    \addToPDFBookmarks{0}{Nomenclature}{g} % OPTIONAL
    \makenomenclature % OPTIONAL
    \printnomenclature[1.25in] % OPTIONAL
    %
    \newpage
    \pagenumbering{arabic}
    \setcounter{page}{1}
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % INCLUDE THE CHAPTERS STARTING WITH THE NOMENCLATURE IF PRESENT
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    \include{front-matter/nomenclature} % OPTIONAL
    \include{chapters/chapter-1}
    \include{chapters/chapter-2}
    \include{chapters/chapter-3}
    \include{chapters/chapter-4}
    \include{chapters/chapter-5}
    \include{chapters/chapter-6}
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % BIBLIOGRAPHY
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        \makeBibliographyPage % make the bibliography title page - can be edited in ut-thesis-template.tex
        \bibliographystyle{agsm} % bibliography style - recommend using apalike-doi as it hyperlinks DOIs
        \bibliography{references/references-dissertation,references/chapter_5} % references.bib included in the references directory
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % APPENDIX - OPTIONAL - COMMENT IF NOT NEEDED
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    \makeAppendixPage   % make the appendix title page - can be edited in ut-thesis-template.tex
    \appendix
    \include{back-matter/appendix-1}
    \include{back-matter/appendix-2}
    %\include{back-matter/appendix-3}
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % A VITA IS REQUIRED
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    \addToTOC{Vita}
    \include{back-matter/vita}
\end{document}