I have index.tex that I made a copy of it. renamed the copy to index_bad.tex, and added the line
\usepackage[pdfpagelabels]{hyperref}
to its preamble. So the 2 files are identical other than this one change.
Then compiled index.tex with pdflatex 3 time and looked at the index.pdf, and it is ok. (i.e. no blank page).
Compiled index_bad.tex with pdflatex 3 times. Now index_bad.pdf has an extra blank page inserted between first section and the second section.
This is the general layout of the document:
\documentclass[12pt]{article}
\usepackage{tikz}
\usepackage{fancyvrb}
\usepackage{graphicx}
\usepackage[left=.7in,right=.5in,top=.7in,bottom=.9in]{geometry}
\usepackage[pdfpagelabels]{hyperref}
\begin{document}
....
\section{....}
\subsection{...}
\begin{Verbatim}[frame=single,framesep=1mm,samepage=true,fontsize=\footnotesize]
.....
\begin{Verbatim}[frame=single,framesep=1mm,samepage=true,fontsize=\footnotesize]
....
\end{document}
When including hyperref a blank page shows up between first section, and the second section. No blank page shows up when this package is not included.
question is why does this happen? and how to fix it?
Since this document includes 2 images and large verbatim, I've zipped the whole folder so it is all self contained.
Unziping the zip file will create a folder. Inside the folder there is index.tex and index_bad.tex and the 2 images used. Running pdflatex on the files will show the problem above.
The zip file is http://12000.org/tmp/072113/latex_problem.zip
Using TL 2013 on Linux mint virtual machine hosted on windows.

Verbatimframes are too large, since they visibly overflow into the page footer. That's what it causing the blank page, most likely. – Werner Jul 22 '13 at 04:25