Error in generating pdflatex from Doxygen output

I’m using Doxygen in order to document my program.
The Doxygen create a lot of tex file and I’m using TeX Live in order to generate a pdf file from the tex files.

It has been worked before but now, after little changes in my source code there is compilation warnings of the latex and it fail to compile although there is no problem with the Doxygen documentation.

The new warnings are:

`LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

And a lot of warnings like:

`LaTeX Warning: Reference `LastPage' on page 60 undefined on input line 170`.

The compilation end with:

make: *** [refman.pdf] Error 1
 exit code: 2(0 for SUCCESS).loggingLevel: 20. Build will exit.

I tried to rerun a few times and there isn’t a change.
Can anyone help me with it?

edit:
This is my main tex file :

documentclass[oneside]{book}

% Packages required by doxygen
usepackage{calc}
usepackage{doxygen}
usepackage{graphicx}
usepackage[utf8]{inputenc}
usepackage{makeidx}
usepackage{multicol}
usepackage{multirow}
usepackage{textcomp}
usepackage[table]{xcolor}

% Font selection
usepackage[T1]{fontenc}
usepackage{mathptmx}
usepackage[scaled=.90]{helvet}
usepackage{courier}
usepackage{amssymb}
usepackage{sectsty}
renewcommand{familydefault}{sfdefault}
allsectionsfont{%
  fontseries{bc}selectfont%
  color{darkgray}%
}
renewcommand{DoxyLabelFont}{%
  fontseries{bc}selectfont%
  color{darkgray}%
}

% Page & text layout

usepackage{geometry}
geometry{%
  a4paper,%
  top=2.5cm,%
  bottom=3.5cm,%
  left=2.5cm,%
  right=2.5cm,%
  headheight=2.5cm%
}
tolerance=750
hfuzz=15pt
hbadness=750
setlength{emergencystretch}{15pt}
setlength{parindent}{0cm}
setlength{parskip}{0.2cm}
makeatletter
renewcommand{paragraph}{%
  @startsection{paragraph}{4}{0ex}{-1.0ex}{1.0ex}{%
    normalfontnormalsizebfseriesSS@parafont%
  }%
}
renewcommand{subparagraph}{%
  @startsection{subparagraph}{5}{0ex}{-1.0ex}{1.0ex}{%
    normalfontnormalsizebfseriesSS@subparafont%
  }%
}
makeatother

% Headers & footers
usepackage{fancyhdr}
usepackage{lastpage}
pagestyle{fancy}
lhead{includegraphics[width=3cm]{doxygen-logo-header.jpg}}
rhead{Page thepage   of pageref{LastPage}}
chead{fancyplain{}{massage}}
lfoot{fancyplain{}{massage2}}
cfoot{fancyplain{}{massage3}}
rfoot{fancyplain{}{massage4}}
renewcommand{footrulewidth}{0.4pt}
renewcommand{chaptermark}[1]{%
  markboth{#1}{}%
}
renewcommand{sectionmark}[1]{%
  markright{thesection #1}%
}

% Indices & bibliography
usepackage{natbib}
usepackage[titles]{tocloft}
setcounter{tocdepth}{3}
setcounter{secnumdepth}{5}
makeindex

% Hyperlinks (required, but should be loaded last)
usepackage{ifpdf}
ifpdf
  usepackage[pdftex,pagebackref=true]{hyperref}
else
  usepackage[ps2pdf,pagebackref=true]{hyperref}
fi
hypersetup{%
  colorlinks=true,%
  linkcolor=blue,%
  citecolor=blue,%
  unicode%
}

% Custom commands
newcommand{clearemptydoublepage}{%
  newpage{pagestyle{empty}cleardoublepage}%
}


%===== C O N T E N T S =====

begin{document}

% Titlepage & ToC

pagestyle{empty}
hypersetup{pageanchor=false}
pagenumbering{roman}
begin{titlepage}
vspace*{7cm}
begin{center}%
includegraphics{doxygen-logo-pdf.jpg}[1cm]
{Huge Library Reference }
vspace*{1.5cm}
{Large COMPANY}
{large VERSION }
vspace*{1cm}
end{center}
end{titlepage}
fancypagestyle{plain}{fancyhf{}%
  renewcommand{headrulewidth}{0pt}
  renewcommand{footrulewidth}{0pt}}
tableofcontents
clearemptydoublepage
pagenumbering{arabic}
hypersetup{pageanchor=true}
pagestyle{fancy}

%--- Begin generated contents ---
chapter{Module Index}
input{modules}
chapter{Data Structure Index}
input{annotated}
chapter{File Index}
input{files}
chapter{Module Documentation}
input{group}
chapter{Data Structure Documentation}
input{struct}
chapter{File Documentation}
input{file}

%--- End generated contents ---

% Index
newpage
phantomsection
addcontentsline{toc}{part}{Index}
printindex

end{document}

It seems like the problem is in the Page & text layout, if I change the "bottom=3.5cm,%" to be "bottom=2.5cm,%" it works.
I don’t know if that was the problem or this only a way to work around the real problem, I’m looking for a long time solution because my source files change frequently and I don’t want to change the tex file every time.

I will be glad to here if you find problems in my tex file or have an idea to the cause of my problem.
Thank you!