The following example illustrates the incompatibility of nccmath/fleqn and hyperref
\documentclass{article}
\usepackage{nccmath}
\numberwithin{equation}{section}
\setlength{\parindent}{0.0ex}
% comment out hyperref to see proper equation references
\usepackage[colorlinks=true]{hyperref}
\begin{document}
\section{First section}
Hello world
\begin{fleqn}
\begin{equation}\label{eqnA}
\qquad\text{equation A:}\quad x + 3y = 7
\end{equation}
\end{fleqn}
\vspace{5in}
Goodby world
\begin{fleqn}
\begin{equation}\label{eqnB}
\qquad\text{equation B:}\quad 5x + 2y = 3
\end{equation}
\end{fleqn}
\newpage
\section{Second section}
reference to equation B: \eqref{eqnB}\\
reference to equation A: \eqref{eqnA}
\end{document}

\documentclassand ending with\end{document}that demonstrates this behavior. Often times, it is the packages that are loaded with the document that affect the result. Welcome to the site. – Steven B. Segletes Apr 08 '14 at 14:08nccmathpackage package but ran into numerous issues that I decided to drop it. See Is there a replacement for nccmath? and the problems listed in the question. If all you want is thefelqnenvironment, you can use Stefan Kottwitz's solution from nccmath affecting minipage widths. – Peter Grill Apr 09 '14 at 16:35